Multiscale QM/MM modelling of catalytic systems with ChemShell

You, Long; Sen, Kakali; Yong, Chin W.; Gunn, David; Purton, John A.; Guan, Jingcheng; Desmoutier, Alec; Nasir, Jamal Abdul; Zhang, Xingfan; Li, Zhu; HOU, QING; Jackson-Masters, Joe; Watts, Sam; Hanson, Rowan; Thomas, Harry N.; Jayawardena, Omal; Logsdail, Andrew J.; Woodley, Scott M.; Senn, Hans Martin; Sherwood, Paul; Catlow, C. R. A.; Sokol, Alexey A.; Keal, Thomas W.

doi:10.1039/d3cp00648d

Cited by 14 publications

(8 citation statements)

References 242 publications

(291 reference statements)

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“…The Py-ChemShell ,, software package is used to cut hemispherical clusters of radius 20.0 a 0 (and active radius 10.0 a 0 ) from the PBE +TS -optimized periodic models of the surface. Figure details the cutting and partitioning processes necessary to convert a periodic surface model into an embedded cluster with QM and MM regions.…”

Section: Methodsmentioning

confidence: 99%

“…The FHI-aims electronic structure package enables highly efficient computation of both periodic and aperiodic systems within the same numerical framework, allowing for direct comparisons to be made. QM/MM energies are calculated using an additive scheme and the hydrogen link-atom approach is used to treat cleaved covalent interactions across the QM–MM interface, both as implemented within the Py-ChemShell , software. The keyword, which is a rescaling coefficient for van der Waals (vdW) radii to determine bonding interactions, was set to a value of 1.3 for all QM/MM calculations to ensure the correct hydrogen saturation of the QM region for the FHI-aims calculation.…”

Section: Methodsmentioning

confidence: 99%

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Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces

2023

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Polycrystalline boron-doped diamond (BDD) is widely used as a working electrode material in electrochemistry, and its properties, such as its stability, make it an appealing support material for nanostructures in electrocatalytic applications. Recent experiments have shown that electrodeposition can lead to the creation of stable small nanoclusters and even single gold adatoms on the BDD surfaces. We investigate the adsorption energy and kinetic stability of single gold atoms adsorbed onto an atomistic model of BDD surfaces by using density functional theory. The surface model is constructed using hybrid quantum mechanics/ molecular mechanics embedding techniques and is based on an oxygen-terminated diamond (110) surface. We use the hybrid quantum mechanics/molecular mechanics method to assess the ability of different density functional approximations to predict the adsorption structure, energy, and barrier for diffusion on pristine and defective surfaces. We find that surface defects (vacancies and surface dopants) strongly anchor adatoms on vacancy sites. We further investigated the thermal stability of gold adatoms, which reveals high barriers associated with lateral diffusion away from the vacancy site. The result provides an explanation for the high stability of experimentally imaged single gold adatoms on BDD and a starting point to investigate the early stages of nucleation during metal surface deposition.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces

2023

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“…Hybrid methods will be detailed in Section 4.4. Many popular codes include QM/MM implementations including Gaussian, 69 CP2K, 68 ORCA, 51 FHI-aims, 59 DFTB+, 70 COBRAMM, 71 ChemShell, 72 and, most recently, xTB. 73…”

Section: Periodic and Molecular Perspectivesmentioning

confidence: 99%

Simulating excited states in metal organic frameworks: from light-absorption to photochemical CO₂ reduction

Ingham,

Aziz,

Di Tommaso

et al. 2023

Mater. Adv.

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“…These could create challenges for the aforementioned treatment methods. Instead, embedded cluster methods, also known as ionic embedded cluster methods for ionically bonded systems, can be combined with the QM/MM approach to provide a practical solution for simulating QM/MM systems of this nature; calculations carried out through this way are called QM/MM embedded cluster calculations. , (Note that the embedded cluster methods can also be used separately to perform embedded cluster calculations.) In (QM/MM) embedded cluster calculations, effective core potentials (ECPs) can be placed adjacent to the boundary of the cluster (i.e., QM region in QM/MM calculations), more specifically, at the positions of the cations surrounding the cluster, to better reproduce the electrostatic feature at the central region of the cluster and to prevent charge spreading .…”

Section: Introductionmentioning

confidence: 99%

“…In (QM/MM) embedded cluster calculations, effective core potentials (ECPs) can be placed adjacent to the boundary of the cluster (i.e., QM region in QM/MM calculations), more specifically, at the positions of the cations surrounding the cluster, to better reproduce the electrostatic feature at the central region of the cluster and to prevent charge spreading . In most cases, a large-core ECP of the corresponding metal in the metal oxide is employed for boundary ECPs. − Alternatively, specially tailored ECPs can be used to improve the results. − …”

Section: Introductionmentioning

confidence: 99%

Level-Shifted Embedded Cluster Method for Modeling the Chemistry of Metal Oxides

Yang,

2024

J. Chem. Theory Comput.

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The embedded cluster method has been used extensively in the study of the chemical and physical properties of metal oxides. This method has been a popular tool due to its relatively high accuracy and low computational cost. An even more promising option may entail integrating the embedded cluster method with the combined quantum mechanical and molecular mechanical (QM/MM) approach, thereby enabling further consideration of interactions within the entire system for superior results. We aim to accurately model the chemistry of metal oxides using this combined scheme. Here, using the prototypical MgO(100) surface as a test system, with Mg 9 O 14 as the cluster in the quantum mechanical region, we show that the embedded cluster with untailored boundary effective core potentials (ECPs) can have frontier orbital energy levels that substantially deviate from the quantum mechanical reference results. This occurs even when Mg 9 O 9 , which retains the stoichiometry of MgO, is used as the cluster in the quantum mechanical region. As a result, the chemical properties of the embedded cluster models differ from those of the quantum mechanical reference model. To address this issue, we propose a new variant of the embedded cluster method called the level-shifted embedded cluster (LSEC) method, which allows the energy levels to be shifted to match the reference levels by tuning the boundary ECPs. Our validation calculations on the adsorption of various adsorbates with different properties on the MgO(100) surface show that the overall performance of QM/MM with the LSEC method is excellent for the adsorption energies, geometries, and charge properties. The excellent performance holds for both the nonstoichiometric and stoichiometric clusters (i.e., Mg 9 O 14 and Mg 9 O 9 , respectively), demonstrating the robustness of the LSEC method. We expect that the LSEC method can be combined with QM/MM or used separately for future chemical studies of metal oxides and other ionically bonded systems.

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Multiscale QM/MM modelling of catalytic systems with ChemShell

Abstract: Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occuring at...

Cited by 14 publications

References 242 publications

Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces

Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces

Simulating excited states in metal organic frameworks: from light-absorption to photochemical CO₂ reduction

Level-Shifted Embedded Cluster Method for Modeling the Chemistry of Metal Oxides

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Multiscale QM/MM modelling of catalytic systems with ChemShell

Abstract: Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occuring at...

Cited by 14 publications

References 242 publications

Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces

Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces

Simulating excited states in metal organic frameworks: from light-absorption to photochemical CO2 reduction

Level-Shifted Embedded Cluster Method for Modeling the Chemistry of Metal Oxides

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Product

Resources

About

Simulating excited states in metal organic frameworks: from light-absorption to photochemical CO₂ reduction