Free-energy calculations of elemental sulphur crystals via molecular dynamics simulations

Pastorino, Claudio; Gamba, Z.

doi:10.1063/1.1582840

Cited by 10 publications

(10 citation statements)

References 32 publications

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“…where is the potential energy, are vibrational frequencies, and ( ) is the vibrational (phonon) density of states (PDOS). [71][72][73] ( ) is normalized such that ∫ ( )d = 3 where is the number of atoms in the sytem. 71 To apply Eq.…”

Section: Free Energymentioning

confidence: 99%

“…1 we needed to calculate the PDOS for each MOF, which we did by Fourier-transforming the velocity autocorrelation function (VACF). 72,73 Each VACF was computed from a short (10 ps) NPT ensemble MD simulation with a Nosé-Hoover thermostat (damping parameter of 100 timesteps) and barostat (damping parameter of 1000 timesteps). For these NPT simulations we used a temperature of 300 K and zero pressure to allow direct comparison with Frenkel-Ladd path free energies.…”

Section: Free Energymentioning

confidence: 99%

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Large-Scale Free Energy Calculations on a Computational Metal–Organic Frameworks Database: Toward Synthetic Likelihood Predictions

Anderson

Gómez-Gualdrón

2020

Chem. Mater.

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Metal-organic frameworks (MOFs) have captivated the research community due to a modular crystal structure that is tailorable for many applications. However, with millions of possible MOFs to be considered, it is challenging to identify the ideal MOF for the application of choice. Although computational screening of MOF databases has provided a fast way to evaluate MOF properties, validation experiments on predicted "exceptional" MOFs are not common due to uncertainties on the synthetic likelihood of computationally constructed MOFs, hence hindering material discovery. Aiming to leverage the perspective provided by large datasets, here we created and screened a topologically diverse database of 8,500 MOFs to interrogate whether thermodynamic stability metrics such as free energy could be used to generally predict the synthetic likelihood of computationally constructed MOFs. To this end, we first evaluated the suitability of two methods and three force fields to calculate free energies in MOFs at large scale, settling on the Frenkel-Ladd path thermodynamic integration method and the UFF4MOF force field. Upon defining a relative free energy, ∆LMFFL, that corrects for some force field artifacts specific to MOF nodes, we found that previously synthesized MOFs tended to cluster in a region below ∆LMFFL = 4.4 kJ/mol per atom, suggesting a general first filter to discriminate between synthetically likely and unlikely MOFs. However, a second filter is needed when several MOF isomorphs are below the ∆LMFFL threshold. In 84% of the cases, the synthetically accessible MOF within an isomorphic series presented the lowest predicted free energy. The present work suggests that crystal free energies could be key to understanding synthetic likelihood for MOFs in computational databases (and MOFs in general), and that the thermodynamics stability of the fully assembled MOF often determines synthetic accessibility.

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Section: Free Energymentioning

confidence: 99%

Section: Free Energymentioning

confidence: 99%

Large-Scale Free Energy Calculations on a Computational Metal–Organic Frameworks Database: Toward Synthetic Likelihood Predictions

Anderson

Gómez-Gualdrón

2020

Chem. Mater.

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“…max where 𝑈 is the potential energy, 𝜈 are vibrational frequencies, and 𝐷(𝜈) is the vibrational (phonon) density of states (PDOS). [71][72][73] 𝐷(𝜈) is normalized such that ∫ 𝐷(𝜈)d𝑣 = 3𝑁 where 𝑁 is the number of atoms in the sytem. 71 To apply Eq.…”

Section: Methodsmentioning

confidence: 99%

Large-Scale Free Energy Calculations on a Computational MOF Database: Toward Synthetic Likelihood Predictions

Anderson¹,

Gómez-Gualdrón

2020

Preprint

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Metal-organic frameworks (MOFs) have captivated the research community due to a modular crystal structure that is tailorable for many applications. However, with millions of possible MOFs to be considered, it is challenging to identify the ideal MOF for the application of choice. Although computational screening of MOF databases has provided a fast way to evaluate MOF properties, validation experiments on predicted “exceptional” MOFs are not common due to uncertainties on the synthetic likelihood of computationally constructed MOFs, hence hindering material discovery. Aiming to leverage the perspective provided by large datasets, here we created and screened a topologically diverse database of 8,500 MOFs to interrogate whether thermodynamic stability metrics such as free energy could be used to generally predict the synthetic likelihood of computationally constructed MOFs. To this end, we first evaluated the suitability of two methods and three force fields to calculate free energies in MOFs at large scale, settling on the Frenkel-Ladd path thermodynamic integration method and the UFF4MOF force field. Upon defining a relative free energy, ΔLMFFL, that corrects for some force field artifacts specific to MOF nodes, we found that previously synthesized MOFs tended to cluster in a region below ΔLMFFL = 4.4 kJ/mol per atom, suggesting a general first filter to discriminate between synthetically likely and unlikely MOFs. However, a second filter is needed when several MOF isomorphs are below the ΔLMFFL threshold. In 84% of the cases, the synthetically accessible MOF within an isomorphic series presented the lowest predicted free energy. The present; work suggests that crystal free energies could be key to understanding synthetic likelihood for MOFs in computational databases (and MOFs in general), and that the thermodynamics stability of the fully assembled MOF often determines synthetic accessibility.

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“…(1) in a robust way is the calculation of F host , the free energy of the porous structure when no adsorbed molecules are present. Assuming that a force field that allows MD simulations of the porous structure to be performed is available, this free energy can be calculated, within the quasiharmonic approximation, 10,13 by using data from a single MD simulation. This method has been used, for example, to calculate the free energy of several phases of elemental sulphur, 13 where it showed good efficiency and reliability compared with more demanding thermodynamic integration methods.…”

Section: Methodsmentioning

confidence: 99%

“…where ν is the vibrational frequency. By assuming the porous host is a harmonic crystal, the free energy can then be calculated 10,13 using…”

Section: Methodsmentioning

confidence: 99%

Osmotic ensemble methods for predicting adsorption-induced structural transitions in nanoporous materials using molecular simulations

Zang

Nair

Sholl

2011

The Journal of Chemical Physics

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Osmotic framework adsorbed solution theory is a useful molecular simulation method to predict the evolution of structural transitions upon adsorption of guest molecules in flexible nanoporous solids. One challenge with previous uses of this approach has been the estimation of free energy differences between the solid phases of interest in the absence of adsorbed molecules. Here we demonstrate that these free energy differences can be calculated without reference to experimental data via the vibrational density of states of each phase, a quantity that can be obtained from molecular dynamics simulations. We show the applicability of this method through case studies of the swelling behaviors of two representative systems in which swelling upon adsorption of water is of importance: single-walled aluminosilicate nanotube bundles and cesium montmorillonite. The resulting predictions show that the aluminosilicate nanotube bundles swell significantly with increasing interstitial adsorption and that the layer spacing of cesium montmorillonite expands up to about 12.5 Å, giving good agreement with experiments. The method is applicable to a wide range of flexible nanoporous materials, such as zeolites, metal-organic frameworks, and layered oxide materials, when candidate structures can be defined and a force field to describe the material is available.

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Free-energy calculations of elemental sulphur crystals via molecular dynamics simulations

Cited by 10 publications

References 32 publications

Large-Scale Free Energy Calculations on a Computational Metal–Organic Frameworks Database: Toward Synthetic Likelihood Predictions

Large-Scale Free Energy Calculations on a Computational Metal–Organic Frameworks Database: Toward Synthetic Likelihood Predictions

Large-Scale Free Energy Calculations on a Computational MOF Database: Toward Synthetic Likelihood Predictions

Osmotic ensemble methods for predicting adsorption-induced structural transitions in nanoporous materials using molecular simulations

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