scholarly journals Local Distortions in a Prototypical Zeolite Framework Containing Double Four-Ring Cages: The Role of Framework Composition and Organic Guests

2020 ◽  
Author(s):  
Michael Fischer ◽  
Linus Freymann
Keyword(s):  
Density Functional ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Judicious Choice ◽  
Dynamics Simulations ◽  
The Impact ◽  
Local Distortions ◽  
Framework Composition

<p>Cube-like double four-ring (<i>d4r</i>) cages are among the most frequent building units of zeolites and zeotypes. In materials synthesised in fluoride-containing media, the fluoride anions are preferentially incorporated in these cages. In order to study the impact of framework composition and organic structure-directing agents (OSDAs) on the possible occurrence of local distortions of fluoride-containing <i>d4r</i> cages, density functional theory (DFT) calculations and DFT-based molecular dynamics simulations were performed for AST-type zeotypes, considering four different compositions (SiO<sub>2</sub>, GeO<sub>2</sub>, AlPO<sub>4</sub>, GaPO<sub>4</sub>) and two different OSDA cations (tetramethylammonium [TMA] and quinuclidinium [QNU]). All systems except SiO<sub>2</sub>-AST show significant deformations, with a pyritohedron-like distortion of the <i>d4r</i> cages occurring in GeO<sub>2</sub>- and GaPO<sub>4</sub>-AST, and a displacement of the fluoride anions towards one of the corners of the cage in AlPO<sub>4</sub>- and GaPO<sub>4</sub>-AST. While the distortions occur at random in TMA-containing zeotypes, they exhibit a preferential orientation in systems that incorporate QNU cations. </p><p>In addition to providing detailed understanding of the local structure of a complex host-guest system on the picosecond timescale, this work indicates the possibility to stabilise ordered distortions through a judicious choice of the OSDA, which might enable a tuning of the material’s properties.</p>

scholarly journals Local Distortions in a Prototypical Zeolite Framework Containing Double Four-Ring Cages: The Role of Framework Composition and Organic Guests

2020 ◽  
Author(s):  
Michael Fischer ◽  
Linus Freymann
Keyword(s):  
Density Functional ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Judicious Choice ◽  
Dynamics Simulations ◽  
The Impact ◽  
Local Distortions ◽  
Framework Composition

<p>Cube-like double four-ring (<i>d4r</i>) cages are among the most frequent building units of zeolites and zeotypes. In materials synthesised in fluoride-containing media, the fluoride anions are preferentially incorporated in these cages. In order to study the impact of framework composition and organic structure-directing agents (OSDAs) on the possible occurrence of local distortions of fluoride-containing <i>d4r</i> cages, density functional theory (DFT) calculations and DFT-based molecular dynamics simulations were performed for AST-type zeotypes, considering four different compositions (SiO<sub>2</sub>, GeO<sub>2</sub>, AlPO<sub>4</sub>, GaPO<sub>4</sub>) and two different OSDA cations (tetramethylammonium [TMA] and quinuclidinium [QNU]). All systems except SiO<sub>2</sub>-AST show significant deformations, with a pyritohedron-like distortion of the <i>d4r</i> cages occurring in GeO<sub>2</sub>- and GaPO<sub>4</sub>-AST, and a displacement of the fluoride anions towards one of the corners of the cage in AlPO<sub>4</sub>- and GaPO<sub>4</sub>-AST. While the distortions occur at random in TMA-containing zeotypes, they exhibit a preferential orientation in systems that incorporate QNU cations. </p><p>In addition to providing detailed understanding of the local structure of a complex host-guest system on the picosecond timescale, this work indicates the possibility to stabilise ordered distortions through a judicious choice of the OSDA, which might enable a tuning of the material’s properties.</p>

scholarly journals Local Distortions in a Prototypical Zeolite Framework Containing Double Four-Ring Cages: The Role of Framework Composition and Organic Guests

2020 ◽  
Author(s):  
Michael Fischer ◽  
Linus Freymann
Keyword(s):  
Density Functional ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Judicious Choice ◽  
Dynamics Simulations ◽  
The Impact ◽  
Local Distortions ◽  
Framework Composition

<p>Cube-like double four-ring (<i>d4r</i>) cages are among the most frequent building units of zeolites and zeotypes. In materials synthesised in fluoride-containing media, the fluoride anions are preferentially incorporated in these cages. In order to study the impact of framework composition and organic structure-directing agents (OSDAs) on the possible occurrence of local distortions of fluoride-containing <i>d4r</i> cages, density functional theory (DFT) calculations and DFT-based molecular dynamics simulations were performed for AST-type zeotypes, considering four different compositions (SiO<sub>2</sub>, GeO<sub>2</sub>, AlPO<sub>4</sub>, GaPO<sub>4</sub>) and two different OSDA cations (tetramethylammonium [TMA] and quinuclidinium [QNU]). All systems except SiO<sub>2</sub>-AST show significant deformations, with a pyritohedron-like distortion of the <i>d4r</i> cages occurring in GeO<sub>2</sub>- and GaPO<sub>4</sub>-AST, and a displacement of the fluoride anions towards one of the corners of the cage in AlPO<sub>4</sub>- and GaPO<sub>4</sub>-AST. While the distortions occur at random in TMA-containing zeotypes, they exhibit a preferential orientation in systems that incorporate QNU cations. </p><p>In addition to providing detailed understanding of the local structure of a complex host-guest system on the picosecond timescale, this work indicates the possibility to stabilise ordered distortions through a judicious choice of the OSDA, which might enable a tuning of the material’s properties.</p>

scholarly journals Accuracy and Reproducibility of Host-Guest Interactions in Zeolites

2020 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Binding Affinities ◽  
Computationally Efficient ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, no benchmark examining these calculation strategies has been reported. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. We show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and together with the reported results, provide robust, reproducible, and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

scholarly journals Accuracy and Reproducibility of Host-Guest Interactions in Zeolites

2020 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Binding Affinities ◽  
Computationally Efficient ◽  
Zeolite Framework ◽  
Functional Theory ◽  
Organic Structure ◽  
Dynamics Simulations

Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, no benchmark examining these calculation strategies has been reported. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. We show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and together with the reported results, provide robust, reproducible, and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

The Role of SiH3 Diffusion in Determining the Surface Smoothness of Plasma-Deposited Amorphous Si Thin Films: An Atomic-Scale Analysis

2005 ◽  
Vol 862 ◽  
Author(s):  
Mayur S. Valipa ◽  
Tamas Bakos ◽  
Eray S. Aydil ◽  
Dimitrios Maroudas
Keyword(s):  
Thin Films ◽  
Density Functional ◽  
Activation Barrier ◽  
Density Functional Theory Calculations ◽  
Atomic Scale ◽  
Functional Theory ◽  
Weak Adsorption ◽  
Dynamics Simulations ◽  
Hydrogenated Amorphous

AbstractDevice-quality hydrogenated amorphous silicon (a-Si:H) thin films grown under conditions where the SiH3 radical is the dominant deposition precursor are remarkably smooth, as the SiH3 radical is very mobile and fills surface valleys during its diffusion on the a-Si:H surface. In this paper, we analyze atomic-scale mechanisms of SiH3 diffusion on a-Si:H surfaces based on molecular-dynamics simulations of SiH3 radical impingement on surfaces of a-Si:H films. The computed average activation barrier for radical diffusion on a-Si:H is 0.16 eV. This low barrier is due to the weak adsorption of the radical onto the a-Si:H surface and its migration predominantly through overcoordination defects; this is consistent with our density functional theory calculations on crystalline Si surfaces. The diffusing SiH3 radical incorporates preferentially into valleys on the a-Si:H surface when it transfers an H atom and forms a Si-Si backbond, even in the absence of dangling bonds.

scholarly journals Dynamics and fragmentation mechanism of (C5H4CH3)Pt(CH3)3 on SiO2 surfaces

2018 ◽  
Vol 9 ◽  
pp. 711-720 ◽  
Author(s):  
Kaliappan Muthukumar ◽  
Harald O Jeschke ◽  
Roser Valentí
Keyword(s):  
Electron Beam ◽  
Active Sites ◽  
Density Functional ◽  
Fragmentation Mechanism ◽  
Functional Theory ◽  
Before And After ◽  
Surface Active ◽  
Dynamics Simulations ◽  
Precursor Molecules

The interaction of trimethyl(methylcyclopentadienyl)platinum(IV) ((C5H4CH3)Pt(CH3)3) molecules on fully and partially hydroxylated SiO2 surfaces, as well as the dynamics of this interaction were investigated using density functional theory (DFT) and finite temperature DFT-based molecular dynamics simulations. Fully and partially hydroxylated surfaces represent substrates before and after electron beam treatment and this study examines the role of electron beam pretreatment on the substrates in the initial stages of precursor dissociation and formation of Pt deposits. Our simulations show that on fully hydroxylated surfaces or untreated surfaces, the precursor molecules remain inactivated while we observe fragmentation of (C5H4CH3)Pt(CH3)3 on partially hydroxylated surfaces. The behavior of precursor molecules on the partially hydroxylated surfaces has been found to depend on the initial orientation of the molecule and the distribution of surface active sites. Based on the observations from the simulations and available experiments, we discuss possible dissociation channels of the precursor.

scholarly journals Fluoride Anions in All-Silica Zeolites: Studying Preferred Fluoride Sites and Dynamic Disorder with Density Functional Theory Calculations

2021 ◽  
Author(s):  
Michael Fischer
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Dynamic Behaviour ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Dynamic Disorder ◽  
Organic Structure ◽  
Molecular Dynamics Calculations ◽  
Structure Calculations

<div>In all-silica zeolites synthesised via the “fluoride route”, the fluoride anions are typically incorporated in small cages, forming [SiO<sub>4</sub>F]<sup>-</sup> trigonal bipyramids. While diffraction and NMR experiments can elucidate the fluoride location(s) and the occurrence/absence of dynamic disorder, they provide limited insights into the factors that determine equilibrium position and dynamic behaviour. To develop a more thorough understanding, electronic structure calculations in the framework of dispersion-corrected density functional theory (DFT) were performed for five all-silica zeolites (NON, STF, IFR, STT, CHA frameworks). DFT-based predictions of the energetically preferred fluoride location within a given cage were mostly in excellent agreement with experiment. Apart from the known tendency of fluoride anions to locate close to small rings, there are no easily generalisable crystal-chemical rules to predict the most probable fluoride sites.</div><div>DFT-based molecular dynamics calculations were employed to predict and explain the dynamic behaviour of the fluoride anions, which differs markedly among the different frameworks. On the basis of the simulations, it could be determined that local interactions of fluoride anions with framework Si atoms have larger impact on the (non-)occurrence of dynamic disorder than longer-range interactions with the organic structure-directing agents. In addition to providing detailed understanding of the behaviour of fluoride anions in as-synthesised all-silica zeolites, the findings of the present work could contribute to a further elucidation of the structure-directing role of fluoride during zeolite synthesis.</div>

scholarly journals Fluoride Anions in All-Silica Zeolites: Studying Preferred Fluoride Sites and Dynamic Disorder with Density Functional Theory Calculations

2021 ◽  
Author(s):  
Michael Fischer
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Dynamic Behaviour ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Dynamic Disorder ◽  
Organic Structure ◽  
Molecular Dynamics Calculations ◽  
Structure Calculations

<div>In all-silica zeolites synthesised via the “fluoride route”, the fluoride anions are typically incorporated in small cages, forming [SiO<sub>4</sub>F]<sup>-</sup> trigonal bipyramids. While diffraction and NMR experiments can elucidate the fluoride location(s) and the occurrence/absence of dynamic disorder, they provide limited insights into the factors that determine equilibrium position and dynamic behaviour. To develop a more thorough understanding, electronic structure calculations in the framework of dispersion-corrected density functional theory (DFT) were performed for five all-silica zeolites (NON, STF, IFR, STT, CHA frameworks). DFT-based predictions of the energetically preferred fluoride location within a given cage were mostly in excellent agreement with experiment. Apart from the known tendency of fluoride anions to locate close to small rings, there are no easily generalisable crystal-chemical rules to predict the most probable fluoride sites.</div><div>DFT-based molecular dynamics calculations were employed to predict and explain the dynamic behaviour of the fluoride anions, which differs markedly among the different frameworks. On the basis of the simulations, it could be determined that local interactions of fluoride anions with framework Si atoms have larger impact on the (non-)occurrence of dynamic disorder than longer-range interactions with the organic structure-directing agents. In addition to providing detailed understanding of the behaviour of fluoride anions in as-synthesised all-silica zeolites, the findings of the present work could contribute to a further elucidation of the structure-directing role of fluoride during zeolite synthesis.</div>

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