Globally Optimized Molecular Embeddings for Dynamic Reaction Solvate Shell Optimization and Active Site Design

Behrens, Dominik; Hartke, Bernd

doi:10.1007/s11244-021-01486-1

Cited by 5 publications

(12 citation statements)

References 35 publications

(40 reference statements)

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“…Decisive for the catalytic effect of local electrostatic potentials V E are their values at or near the reactant nuclei next to the breaking or forming bonds, − i.e., at several locations r⃗ i . For the reaction path or transition state of a given reaction, optimally placed inside a constructed molecular framework cavity, these r⃗ i values are known.…”

Section: Methodsmentioning

confidence: 99%

“…For the reaction path or transition state of a given reaction, optimally placed inside a constructed molecular framework cavity, these r⃗ i values are known. Now we want to adjust these V E ( r⃗ i ) to catalytically optimal values − by suitable mutations of molecular framework substituents in the cavity periphery. As indicated above, such mutation positions r⃗ j are automatically selected and hence also known.…”

Section: Methodsmentioning

confidence: 99%

“…As with enzymes, both steric features and electric fields are important considerations for the catalytically active site(s) (cf. refs − and references cited therein). Also, spatial confinement by itself is an important modifier of reactivity. , …”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Graph-based Automated Macro-Molecule Assembly

Spenke

Hartke

2022

J. Chem. Inf. Model.

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We present a general molecular framework assembly algorithm that takes a largely arbitrary molecular fragment database and a user-supplied target template graph as input. Automatic assembly of molecular fragments from the database, following a prescribed, user-supplied set of connection rules, then turns the template graph into an actual, chemically reasonable molecular framework. Assembly capabilities of our algorithm are tested by producing several abstract, closed-loop shapes. To indicate a few of many possible application areas we demonstrate a host–guest complex and a road toward catalysis. Postassembly substituent exchange can be used to produce electric fields of desired values at desired points inside the framework or at its surface as a stepping stone toward rationally designed, artificial heterogeneous catalysts.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Graph-based Automated Macro-Molecule Assembly

Spenke

Hartke

2022

J. Chem. Inf. Model.

Self Cite

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“…For example, we have proposed the inverse-design approach Gradient-driven Molecule Construction (GdMC) [301][302][303], which targets design of new catalysts by sequentially constructing metal fragments that stabilize structurally activated small molecules in intermediates through reduced structure gradients on all atoms. In another approach, Hartke and co-workers have combined optimizations of minimum energy reaction paths in an electric field of point charges with global optimization techniques in their Globally Optimized Catalyst scheme [304,305] and have further improved on it in a quantum-mechanical molecularmechanical composite approach [306].…”

Section: Catalyst Designmentioning

confidence: 99%

Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis

Steiner

Reiher

2022

Top Catal

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Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to catalysis: (i) automation allows one to consider orders of magnitude more structures in a systematic and open-ended fashion than what would be accessible by manual inspection. Eventually, full resolution in terms of structural varieties and conformations as well as with respect to the type and number of potentially important elementary reaction steps (including decomposition reactions that determine turnover numbers) may be achieved. (ii) Fast electronic structure methods with uncertainty quantification warrant high efficiency and reliability in order to not only deliver results quickly, but also to allow for predictive work. (iii) A high degree of autonomy reduces the amount of manual human work, processing errors, and human bias. Although being inherently unbiased, it is still steerable with respect to specific regions of an emerging network and with respect to the addition of new reactant species. This allows for a high fidelity of the formalization of some catalytic process and for surprising in silico discoveries. In this work, we first review the state of the art in computational catalysis to embed autonomous explorations into the general field from which it draws its ingredients. We then elaborate on the specific conceptual issues that arise in the context of autonomous computational procedures, some of which we discuss at an example catalytic system. Graphical Abstract

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“…For example, we have proposed the inverse-design approach Gradient-driven Molecule Construction (GdMC) [293 -295 ], which targets design of new catalysts by sequentially constructing metal fragments that stabilize structurally activated small molecules in intermediates through reduced structure gradients on all atoms. In another approach, Hartke and co-workers have combined optimizations of minimum energy reaction paths in an electric field of point charges with global optimization techniques in their Globally Optimized Catalyst scheme [296 , 297 ] and have further improved on it in a quantum-mechanical molecular-mechanical composite approach [298 ].…”

Section: Catalyst Designmentioning

confidence: 99%

Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis

Steiner,

Reiher

2021

Preprint

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Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to catalysis: (i) automation allows one to consider orders of magnitude more structures than what would be accessible by manual inspection, eventually with full resolution of structural varieties and conformations as well as with respect to the type and number of potentially important elementary reaction steps (including decomposition reactions that determine turnover number), (ii) fast electronic structure methods with uncertainty quantification warrant high efficiency and reliability in order to not only deliver results quickly, but also to allow for predictive work, and (iii) a high degree of autonomy reduces processing errors and human bias. In this work, we first review the state of the art in this research area, then discuss important conceptual issues that eventually determine feasibility and reliability of computational procedures, and finally demonstrate an implementation of these concepts applied to a catalytic system.

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Globally Optimized Molecular Embeddings for Dynamic Reaction Solvate Shell Optimization and Active Site Design

Cited by 5 publications

References 35 publications

Graph-based Automated Macro-Molecule Assembly

Graph-based Automated Macro-Molecule Assembly

Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis

Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis

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