A combined periodic DFT and QM/MM approach to understand the radical mechanism of the catalytic production of methanol from glycerol

Sainna, Mala A.; Nanavati, Sachin P.; Black, Constance; Smith, Louise; Mugford, Karl; Jenkins, H. Donald Brooke; Douthwaite, Mark; Dummer, Nicholas F.; Catlow, Cra; Taylor, Stuart H.; Logsdail, Andrew J.

doi:10.1039/d0fd00005a

Cited by 7 publications

(4 citation statements)

References 52 publications

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“…In contrast, the QM/MM calculations with the CEC method and the embedded Mg 9 O 9 cluster give results in better agreement with the QM reference results, with the maximum deviation and mean unsigned deviation being 0.18 and 0.16 eV, respectively. This has driven many studies to employ a stoichiometric cluster for (QM/MM) embedded cluster calculations. , Additional tests were conducted using different stoichiometric QM clusters, including Mg 9 O 9 , Mg 17 O 17 , and Mg 25 O 25 , along with the modified def2-TZVP basis sets (see Figure S3). The results demonstrate that increasing the size of the stoichiometric QM cluster can improve the adsorption energy, bringing it closer to the QM reference result.…”

Section: Resultsmentioning

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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Section: Resultsmentioning

confidence: 99%

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

Yang,

2024

J. Chem. Theory Comput.

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“…223 Sainna et al used ChemShell to study the reaction of glycerol over a catalytic MgO surface to form methanol. 224 The results indicated that the most favourable route to methanol production involves a disproportionation reaction on the surface of MgO, while water is unlikely to play an important part in the process.…”

Section: Solid State Embeddingmentioning

confidence: 95%

Multiscale QM/MM modelling of catalytic systems with ChemShell

You

Sen

Yong

et al. 2023

Phys. Chem. Chem. Phys.

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“…We emphasize that the systematic determination of QM regions for nonbiomolecular structures (e.g., for heterogeneous catalysis on molecular surfaces) has received only little attention. In these cases, one can either combine a two‐dimensional periodic QM approach with the QM/MM methodology in such a way that the QM/MM boundary does not break the periodicity 232 or employ clusters of atoms 233 as QM regions. The latter option was also applied in the study of covalent organic and metal organic framework structures, in which several unit clusters are taken as the QM region 234–237 …”

Section: Choice and Size Of Qm Regionmentioning

confidence: 99%

UniversalQM/MMapproaches for general nanoscale applications

Csizi

Reiher

2023

WIREs Comput Mol Sci

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Quantum mechanics/molecular mechanics (QM/MM) hybrid models allow one to address chemical phenomena in complex molecular environments. Whereas this modeling approach can cope with a large system size at moderate computational costs, the models are often tedious to construct and require manual preprocessing and expertise. As a result, transferability to new application areas can be limited and the many parameters are not easy to adjust to reference data that are typically scarce. Therefore, it is desirable to devise automated procedures of controllable accuracy, which enables such modeling in a standardized and black‐box‐type manner. Although diverse best‐practice protocols have been set up for the construction of individual components of a QM/MM model (e.g., the MM potential, the type of embedding, the choice of the QM region), automated procedures that reconcile all steps of the QM/MM model construction are still rare. Here, we review the state of the art of QM/MM modeling with a focus on automation. We elaborate on MM model parametrization, on atom‐economical physically‐motivated QM region selection, and on embedding schemes that incorporate mutual polarization as critical components of the QM/MM model. In view of the broad scope of the field, we mostly restrict the discussion to methodologies that build de novo models based on first‐principles data, on uncertainty quantification, and on error mitigation with a high potential for automation. Ultimately, it is desirable to be able to set up reliable QM/MM models in a fast and efficient automated way without being constrained by specific chemical or technical limitations. This article is categorized under: Electronic Structure Theory > Combined QM/MM Methods

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A combined periodic DFT and QM/MM approach to understand the radical mechanism of the catalytic production of methanol from glycerol

Abstract: The production of methanol from glycerol over a basic oxide, such as MgO, using high reaction temperatures (320 °C) is a promising new approach to improving atom efficiency in the...

Cited by 7 publications

References 52 publications

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

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

Multiscale QM/MM modelling of catalytic systems with ChemShell

UniversalQM/MMapproaches for general nanoscale applications

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