Stk: An Extendable Python Framework for Automated Molecular and Supramolecular Structure Assembly and Discovery

Turcani, Lukas; Tarzia, Andrew; Szczypiński, Filip; Jelfs, Kim E.

doi:10.26434/chemrxiv.14179022

Cited by 5 publications

(9 citation statements)

References 50 publications

(59 reference statements)

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“…By simultaneously screening linkers and varying the positions and orientations of the vertices and complex, they designed and synthesized a cage with a higher affinity toward sulfate than any available sulfate receptor synthesized to date. Two prominent open-source cage generation tools with graphical interfaces include stk developed by Jelfs and coworkers 40 and cgbind developed by our group. 41 Both tools generate cages by providing ligands with specified and predefined topology.…”

Section: Quantum Approachesmentioning

confidence: 99%

“…stk was originally designed to generate structures of small linear polymers, porous organic cages, and covalent organic frameworks (Figure 4b). 40,112 However, it has also been extended to rotaxanes, host−guest complexes, metalloorganic cages, and MOFs. 40 The tool uses predefined topological graphs, where the building blocks are placed on the edges and the vertices of the graph.…”

Section: Quantum Approachesmentioning

confidence: 99%

“…40,112 However, it has also been extended to rotaxanes, host−guest complexes, metalloorganic cages, and MOFs. 40 The tool uses predefined topological graphs, where the building blocks are placed on the edges and the vertices of the graph. They are then joined by bonds, and in the case of covalent organic molecules, redundant atoms are removed.…”

Section: Quantum Approachesmentioning

confidence: 99%

“…Efficient computational tools have also emerged to rapidly predict molecular properties, enabling synthetic chemists to quickly screen multiple cage designs before attempting their synthesis in the laboratory. 40,41 Combining computational and experimental efforts could substantially speed up the design of functional metallo-organic cages, reducing time and resources.…”

Section: Introductionmentioning

confidence: 99%

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Computational Modeling of Supramolecular Metallo-organic Cages–Challenges and Opportunities

et al. 2022

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Self-assembled metallo-organic cages have emerged as promising biomimetic platforms that can encapsulate whole substrates akin to an enzyme active site. Extensive experimental work has enabled access to a variety of structures, with a few notable examples showing catalytic behavior. However, computational investigations of metallo-organic cages are scarce, not least due to the challenges associated with their modeling and the lack of accurate and efficient protocols to evaluate these systems. In this review, we discuss key molecular principles governing the design of functional metallo-organic cages, from the assembly of building blocks through binding and catalysis. For each of these processes, computational protocols will be reviewed, considering their inherent strengths and weaknesses. We will demonstrate that while each approach may have its own specific pitfalls, they can be a powerful tool for rationalizing experimental observables and to guide synthetic efforts. To illustrate this point, we present several examples where modeling has helped to elucidate fundamental principles behind molecular recognition and reactivity. We highlight the importance of combining computational and experimental efforts to speed up supramolecular catalyst design while reducing time and resources.

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Section: Quantum Approachesmentioning

confidence: 99%

Section: Quantum Approachesmentioning

confidence: 99%

Section: Quantum Approachesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Computational Modeling of Supramolecular Metallo-organic Cages–Challenges and Opportunities

et al. 2022

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“…[52][53][54][55] Until recently, however, it has not been possible to develop equivalent screening workflows for MOPs because no open-source structure generation software was available. Some of us previously developed the supramolecular toolkit (stk ), 56,57 an open-source Python framework that handles the structure prediction of supramolecular architectures. Here, we highlight the first use of stk to screen candidate MOPs.…”

Section: Introductionmentioning

confidence: 99%

High-throughput Computational Evaluation of Low Symmetry Pd2L4 Cages to Aid in System Design

Tarzia¹,

Lewis

Jelfs³

2021

Preprint

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The use of unsymmetrical components in metallo-supramolecular chemistry allows for low-symmetry architectures with anisotropic cavities toward guest-binding with high specificity and affinity. Unsymmetrical ditopic ligands mixed with Pd(II) have the potential to self-assemble into reduced symmetry Pd2L4 metallo-architectures. Mixtures of isomers can form, however, resulting in potentially undesirable heterogeneity within a system. Therefore it is paramount to be able to design components that preferentially form a single isomer. Previous data suggested that computational methods could predict with reasonable accuracy whether unsymmetrical ligands would preferentially self-assemble into a single isomer under constraints of geometrical mismatch. We successfully apply a collaborative computational and experimental workflow to mitigate costly trial-and-error synthetic approaches. Our low-cost computational workflow rapidly constructs new unsymmetrical ligands (and Pd2L4 cage isomers) and ranks their likelihood for forming cis-Pd2L4 assemblies. From this narrowed search space, we successfully synthesised four new low-symmetry, cis-Pd2L4 cages, with cavities of different shapes and sizes.

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Observation of Rare Tri6Di9 Imine Cages Using Highly Fluorinated Building Blocks

et al. 2022

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The first synthesis of an organic Tri6Di9 cage is presented. Two structurally distinct Tri6Di9 cages were synthesised by combining a highly fluorinated aldehyde with two ditopic amines. Although the pure compound could not be isolated despite many attempts, the information obtained is critical for the future design of large supramolecular structures. Computational and experimental methods indicate that the addition of perfluorinated aromatic linkers in the assembly of porous organic cages opens up new possibilities for influencing the reaction pathway towards rare and unknown structures.

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Stk: An Extendable Python Framework for Automated Molecular and Supramolecular Structure Assembly and Discovery

Cited by 5 publications

References 50 publications

Computational Modeling of Supramolecular Metallo-organic Cages–Challenges and Opportunities

Computational Modeling of Supramolecular Metallo-organic Cages–Challenges and Opportunities

High-throughput Computational Evaluation of Low Symmetry Pd2L4 Cages to Aid in System Design

Observation of Rare Tri6Di9 Imine Cages Using Highly Fluorinated Building Blocks

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