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.

scholarly journals Benchmarking binding energy calculations for organic structure-directing agents in pure-silica zeolites

2021 ◽  
Author(s):  
Daniel Schwalbe-Koda ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Binding Energy ◽  
Density Functional ◽  
Single Point ◽  
Cost Effective ◽  
Binding Energies ◽  
Computationally Efficient ◽  
Organic Structure ◽  
Pure Silica ◽  
Structure Directing Agents ◽  
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, there is no consensus on the best calculation strategy for high-throughput virtual screening undertakings. 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. Enabled by automation software, 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 provide robust and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs.

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>

Theoretical binding affinities and spectra of complexes formed by a cyclic β-peptoid with amino acids

2010 ◽  
Vol 64 (4) ◽  
Author(s):  
Yu Sun ◽  
Jinpei Du ◽  
Ying Wang ◽  
Shi Wu
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Binding Energies ◽  
Basis Set ◽  
Binding Affinities ◽  
Functional Theory ◽  
Guest Molecules ◽  
The Density Functional Theory ◽  
Optimized Geometries

AbstractBinding affinities of a cyclic β-peptoid to amino acids were studied using the density functional theory (DFT) at the B3LYP/6-311G(d,p) level after the basis set superior error (BSSE). The host molecule possesses binding ability to amino acids since the binding energies of the complexes formed are negative. The complexes were stabilized via hydrogen bonds between the host and the guest molecules. Based on the B3LYP/6-31G(d) optimized geometries, electronic spectra of the complexes were calculated using the INDO/CIS method. 13C NMR spectra and nucleus-independent chemical shift (NICS) values of the complexes were computed at the B3LYP/6-31G(d) level. Carbon atoms in the carboxyl groups of the complexes are shifted downfield relative to those of the host. Some complexes exhibit aromaticity although the host shows anti-aromaticity. Formation of hydrogen bonds leads to cyclic current formation in these complexes.

Graphene adlayer growth between nonepitaxial graphene and Ni(111) substrate: a promising theoretical scheme

2020 ◽  
Author(s):  
Lijuan Meng ◽  
Jinlian Lu ◽  
Yujie Bai ◽  
Lili Liu ◽  
Tang Jingyi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Chemical Vapor Deposition ◽  
Molecular Dynamics Simulations ◽  
Vapor Deposition ◽  
Density Functional ◽  
Chemical Vapor ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Dynamics Simulations

Understanding the fundamentals of chemical vapor deposition bilayer graphene growth is crucial for its synthesis. By employing density functional theory calculations and classical molecular dynamics simulations, we have investigated the...

scholarly journals A Comparative Study of Oxygen and Hydrogen Adsorption on Strained and Alloy-Supported Pt(111) Monolayers

2021 ◽  
Vol 7 (7) ◽  
pp. 101
Author(s):  
Ian Shuttleworth
Keyword(s):  
Comparative Study ◽  
Density Functional ◽  
Hydrogen Adsorption ◽  
Binding Energies ◽  
High Symmetry ◽  
Density Functionals ◽  
Functional Theory ◽  
Ligand Effects ◽  
Ferromagnetic Alloys ◽  
Depth Study

A comparative study of the unreacted and reacted uniaxially strained Pt(111) and the layered (111)-Pt/Ni/Pt3Ni and (111)-Pt/Ni/PtNi3 surfaces has been performed using density functional theory (DFT). An in-depth study of the unreacted surfaces has been performed to evaluate the importance of geometric, magnetic and ligand effects in determining the reactivity of these different Pt surfaces. An analysis of the binding energies of oxygen and hydrogen over the high-symmetry binding positions of all surfaces has been performed. The study has shown that O and H tend to bind more strongly to the (111)-Pt/Ni/Pt3Ni surface and less strongly to the (111)-Pt/Ni/PtNi3 surface compared to binding on the equivalently strained Pt(111) surfaces. Changes in the surface magnetisation of the surfaces overlaying the ferromagnetic alloys during adsorption are discussed, as well as the behaviour of the d-band centre across all surfaces, to evaluate the potential mechanisms for these differences in binding. An accompanying comparison of the accessible density functionals has been included to estimate the error in the computational binding energies.

A DFT study of spherands containing five anisyl groups — Highly preorganized to bind the alkali metal

2006 ◽  
Vol 84 (8) ◽  
pp. 1045-1049 ◽  
Author(s):  
Shabaan AK Elroby ◽  
Kyu Hwan Lee ◽  
Seung Joo Cho ◽  
Alan Hinchliffe
Keyword(s):  
Density Functional Theory ◽  
Binding Energy ◽  
Density Functional ◽  
Ionic Radius ◽  
Binding Energies ◽  
Cavity Size ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Good Agreement

Although anisyl units are basically poor ligands for metal ions, the rigid placements of their oxygens during synthesis rather than during complexation are undoubtedly responsible for the enhanced binding and selectivity of the spherand. We used standard B3LYP/6-31G** (5d) density functional theory (DFT) to investigate the complexation between spherands containing five anisyl groups, with CH2–O–CH2 (2) and CH2–S–CH2 (3) units in an 18-membered macrocyclic ring, and the cationic guests (Li+, Na+, and K+). Our geometric structure results for spherands 1, 2, and 3 are in good agreement with the previously reported X-ray diffraction data. The absolute values of the binding energy of all the spherands are inversely proportional to the ionic radius of the guests. The results, taken as a whole, show that replacement of one anisyl group by CH2–O–CH2 (2) and CH2–S–CH2 (3) makes the cavity bigger and less preorganized. In addition, both the binding and specificity decrease for small ions. The spherands 2 and 3 appear beautifully preorganized to bind all guests, so it is not surprising that their binding energies are close to the parent spherand 1. Interestingly, there is a clear linear relation between the radius of the cavity and the binding energy (R2 = 0.999).Key words: spherands, preorganization, density functional theory, binding energy, cavity size.

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