Profile Details

Create Project

★★★★★

☆☆☆☆☆

USD 60 /hr

★★★★★

☆☆☆☆☆

Hire Dr. David P.

United States

USD 60 /hr

I am a scientist in chemistry, biochemistry, and catalysis willing to assist with you with research soolutions.

Profile Summary

My background coverde diverse fields of chemistry and biochemistry including catalysis, molecular simulations, drug development, and analytical chem.

Subject Matter Expertise

• ☆ Chemical Reagent Development
• ☆ Catalysis
• ☆ Mathematical Chemistry
• ☆ Biocatalysis
• ☆ Coordination Compounds
• ☆ Inorganic Chemistry
• ☆ Physical Chemistry
• ☆ Chemoinformatics
• ☆ Green Chemistry
• ☆ Organometallic Chemistry
• ☆ Quantum Chemistry
• ☆ Theoretical Chemistry
• ☆ Computational Chemistry
• ☆ Biochemistry
• ☆ Immunoassay
• ☆ Biochemical Assays
• ☆ Structural Biology
• ☆ Enzyme Activity Assays
• ☆ Binding Assays
• ☆ Applied Chemistry
• ☆ Python
• ☆ Matlab
• ☆ Scikit-learn

Services

• Writing
• Research
• Consulting
• Data & AI
• Product Development

Writing Technical Writing, General Proofreading & Editing

Research Fact Checking, Scientific and Technical Research, Systematic Literature Review, Secondary Data Collection

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis

Product Development Quality Assurance & Control (QA/QC), Concept Development

Work Experience

Vrije Universiteit Amsterdam

- Present

Senior Researcher

Vrije Universitaet, Amsterdam

January 2022 - Present

Education

PhD (Chemistry)

University of Amsterdam

November 2016 - November 2022

Certifications

• Basis Kwalificatie Onderwijs

  Vrije Universiteit Amsterdam

  June 2023 - Present

Publications

PREPRINT

Noëmi-Feline Ettema, David Alonzo Poole III (2025). Evaluating Docking Approaches for Prediction of Cyclodextrin and Cucurbituril Host-Guest Complex Structures .

Noëmi-Feline Ettema, David Alonzo Poole III (2025). Evaluating Docking Approaches for Prediction of Cyclodextrin and Cucurbituril Host-Guest Complex Structures .

David Poole, Naomi-Feline Ettema (2025). Evaluating Docking Approaches for Prediction of Cyclodextrin and Cucurbituril Host-Guest Complex Structures .

JOURNAL ARTICLE

Peter Kotanko, David Alonzo Poole, Beatriz Akemi Kondo Van Spitzenbergen, Nadja Grobe, Paul Jennings, Andrea Novais Moreno-Amaral (2025). A Self-Reinforcing Pathway Linking PIEZO1 and 3-Carboxy-4-Methyl-5-Propyl-2-Furanpropionate, a Renal Retention Solute, with CKD Progression . Journal of the American Society of Nephrology.

T. Bouwens, E. O. Bobylev, L. S. D. Antony, D. A. Poole, III, E. Alarcón-Lladó, S. Mathew, J. N. H. Reek (2025). Exo-templating via pseudorotaxane formation reduces pathway complexity in the multicomponent self-assembly of M12L24 nanospheres . Nature Chemistry.

Exo-templating via pseudorotaxane formation reduces pathway complexity in the multicomponent self-assembly of M12L24 nanospheres @article{4f3428c1e12b48db830ead1f4f21023f, title = "Exo-templating via pseudorotaxane formation reduces pathway complexity in the multicomponent self-assembly of M12L24 nanospheres", abstract = "Selective formation of multicomponent structures via the self-assembly of numerous building blocks is ubiquitous in biological systems but challenging to emulate synthetically. More components introduce additional possibilities for kinetic intermediates with trap-state ability, hampering access to desired products. In covalent chemistry, templates, reagents and catalysts are applied to create alternative pathways for desired product formation. Analogously, we enlist exo-templating to mould the formation of large, multicomponent supramolecular structures. Specifically, a charged ring docks at 1,5-dioxynaphthalene stations within exo-functionalized building blocks to promote formation of cuboctahedral Pd12L24 nanospheres via exoskeletal templating. With the exo-templating ring present, nanosphere formation occurs via small Pdx–Ly oligomers, while in the absence of the ring a Pdx–Ly polymer resting state rapidly evolves, from which nanosphere formation occurs slowly. We demonstrate a form of kinetic templating—via intermediate destabilization—resembling properties observed in catalysis. Importantly, unlike typically employed endo-templates, we demonstrate that exo-templating is particularly suited for larger, complex, self-assembled structures. (Figure presented.)", author = "T. Bouwens and Bobylev, \{E. O.\} and Antony, \{L. S.D.\} and Poole, \{D. A.\} and E. Alarc{\'o}n-Llad{\'o} and S. Mathew and Reek, \{J. N.H.\}", note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive licence to Springer Nature Limited 2025.", year = "2025", month = jul, doi = "10.1038/s41557-025-01808-w", language = "English", volume = "17", pages = "1067--1075", journal = "Nature Chemistry", issn = "1755-4330", publisher = "Nature Publishing Group", number = "7", } . Nature Chemistry.

Computational Strategies for Broad Spectrum Venom Phospholipase A2 Inhibitors @article{29aa2fa9e7064103ad6ad29c06637dca, title = "Computational Strategies for Broad Spectrum Venom Phospholipase A2 Inhibitors", abstract = "Snakebite envenoming is a persistent cause of mortality and morbidity worldwide due to the logistical challenges and costs of current antibody-based treatments. Their persistence motivates a broad interest in the discovery of inhibitors against multispecies venom phospholipase A2 (PLA2), which are underway as an alternative or supplemental treatment to improve health outcomes. Here, we present new computational strategies for improved inhibitor classification for challenging metalloenzyme targets across many species, including both a new method to utilize existing molecular docking, and subsequent data normalization. These methods were improved to support experimental screening efforts estimating the broader efficacy of candidate PLA2 inhibitors against diverse viper and elapid venoms.", author = "Poole, \{David A.\} and Albulescu, \{Laura Oana\} and Jeroen Kool and Casewell, \{Nicholas R.\} and Geerke, \{Daan P.\}", note = "Publisher Copyright: {\textcopyright} 2025 The Authors. Published by American Chemical Society.", year = "2025", month = may, day = "12", doi = "10.1021/acs.jcim.5c00045", language = "English", volume = "65", pages = "4593--4601", journal = "Journal of chemical information and modeling", issn = "1549-9596", publisher = "American Chemical Society", number = "9", } . Journal of chemical information and modeling.

David A. Poole, III, Laura-Oana Albulescu, Jeroen Kool, Nicholas R. Casewell, Daan P. Geerke (2025). Computational Strategies for Broad Spectrum Venom Phospholipase A2 Inhibitors . Journal of Chemical Information and Modeling.

Deep Electron Redistributions Induced by Dual Junctions Facilitating Electroreduction of Dilute Nitrate to Ammonia @article{be45129c47754bb992241fdc74146212, title = "Deep Electron Redistributions Induced by Dual Junctions Facilitating Electroreduction of Dilute Nitrate to Ammonia", abstract = "The electronic states of metal catalysts can be redistributed by the rectifying contact between metal and semiconductor e.g., N-doped carbon (NC), while the interfacial regulation degree is very limited. Herein, a deep electronic state regulation is achieved by constructing a novel double-heterojunctional Co/Co3O4@NC catalyst containing Co/Co3O4 and Co3O4/NC heterojunctions. When used for dilute electrochemical NO3− reduction reaction (NO3RR), the as-prepared Co/Co3O4@NC exhibits an outstanding Faradaic efficiency for NH3 formation (FENH3) of 97.9\%, –0.4 V versus RHE and significant NH3 yield of 303.5 mmol h−1 gcat−1 at –0.6 V at extremely low nitrate concentrations (100 ppm NO3−-N). Experimental and theoretical results reveal that the dual junctions of Co/Co3O4 and Co3O4/NC drive a unidirectional electron transfer from Co to NC (Co→Co3O4→NC), resulting in electron-deficient Co atoms. The electron-deficient Co promotes NO3− adsorption, the rate-determining step (RDS) for NO3RR, facilitating the dilute NO3RR to NH3. The design strategy provides a novel reference for unidirectional multistage regulation of metal electronic states boosting electrochemical dilute NO3RR, which opens up an avenue for deep electronic state regulation of electrocatalyst breaking the limitation of the electronic regulation degree by rectifying contact.", keywords = "deep electron redistributions, dual junctions, electrochemical nitrate reduction, electron deficient Co", author = "Zhang, \{Lu Hua\} and Bo Zhang and Yaohua Hong and Yang You and Yuzhuo Zhou and Jiayu Zhan and Poole, \{David Alonzo\} and Fengshou Yu", note = "Publisher Copyright: {\textcopyright} 2024 Wiley-VCH GmbH.", year = "2024", month = aug, day = "28", doi = "10.1002/smll.202402430", language = "English", volume = "20", pages = "1--8", journal = "Small", issn = "1613-6810", publisher = "Wiley-VCH Verlag", number = "35", } . Small.

Minimally modified human blood coagulation factor X to bypass direct factor Xa inhibitors @article{5790bc0de2ab4200b94a091e374a46ba, title = "Minimally modified human blood coagulation factor X to bypass direct factor Xa inhibitors", abstract = "Background: Direct oral factor (F)Xa inhibitors are widely used as alternatives to conventional vitamin K antagonists in managing venous thromboembolism and nonvalvular atrial fibrillation. Unfortunately, bleeding-related adverse events remain a major concern in clinical practice. In case of bleeding or emergency surgery, rapid-onset reversal agents may be required to counteract the anticoagulant activity. Objectives: The ability of FXa variants to bypass the direct oral FXa inhibitors was assessed. Methods: Human FXa variants were generated through substitution of phenylalanine 174 (F174) for either alanine, isoleucine, or serine. FXa variants were stably expressed in HEK293 cells and purified to homogeneity using ion-exchange chromatography. Results: F174-substituted human FX variants demonstrated efficacy in restoring thrombin generation in plasma containing direct FXa inhibitors (apixaban, rivaroxaban, edoxaban). Their ability to bypass the anticoagulant effects stems from a significantly reduced sensitivity for the direct FXa inhibitors due to a decrease in binding affinity determined using molecular dynamics simulations and free energy computation. Furthermore, F174 modification resulted in a partial loss of inhibition by tissue factor pathway inhibitor, enhancing the procoagulant effect of F174-substituted FX. Consequently, the F174A- and F174S-substituted FX variants effectively counteracted the effects of 2 widely used anticoagulants, apixaban and rivaroxaban, in plasma of atrial fibrillation and venous thromboembolism patients. Conclusion: These human FX variants have the potential to serve as a rescue reversal strategy to overcome the effect of direct FXa inhibitors in case of life-threatening bleeding events or emergency surgical interventions.", keywords = "anticoagulants, antidotes, factor Xa inhibitors, hemorrhage, molecular dynamics simulation", author = "Mark Schreuder and Georges Jourdi and Dejvid Veizaj and Poole, \{David A.\} and Cheung, \{Ka Lei\} and G{\'e}raldine Poenou and Dani{\"e}l Verhoef and Stella Thomassen and Janssen, \{Laura F.H.\} and Alain Stepanian and Hackeng, \{Tilman M.\} and Pascale Gaussem and Reitsma, \{Pieter H.\} and Geerke, \{Daan P.\} and Virginie Siguret and Bos, \{Mettine H.A.\}", note = "Publisher Copyright: {\textcopyright} 2024 The Author(s)", year = "2024", month = aug, doi = "10.1016/j.jtha.2024.04.022", language = "English", volume = "22", pages = "2211--2226", journal = "Journal of Thrombosis and Haemostasis", issn = "1538-7933", publisher = "Elsevier B.V.", number = "8", } . Journal of Thrombosis and Haemostasis.

Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis @article{1a45661a092d41469ba600e3cace84a8, title = "Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis", abstract = "Peptide display technologies are a powerful method for discovery of new bioactive sequences, but linear sequences are often very unstable in a biological setting. Macrocyclisation of such peptides is beneficial for target affinity, selectivity, stability, and cell permeability. However, macrocyclisation of a linear hit is unreliable and requires extensive structural knowledge. Genetically encoding macrocyclisation during the discovery process is a better approach, and so there is a need for diverse cyclisation options that can be deployed in the context of peptide display techniques such as mRNA display. In this work we show that meta-cyanopyridylalanine (mCNP) can be ribosomally incorporated into peptides, forming a macrocycle in a spontaneous and selective reaction with an N-terminal cysteine generated from bypassing the initiation codon in translation. This reactive amino acid can also be easily incorporated into peptides during standard Fmoc solid phase peptide synthesis, which can otherwise be a bottleneck in transferring from peptide discovery to peptide testing and application. We demonstrate the potential of this new method by discovery of macrocyclic peptides targeting influenza haemagglutinin, and molecular dynamics simulation indicates the mCNP cross-link stabilises a beta sheet structure in a representative of the most abundant cluster of active hits. Cyclisation by mCNP is also shown to be compatible with thioether macrocyclisation at a second cysteine to form bicycles of different architectures, provided that cysteine placement reinforces selectivity, with this bicyclisation happening spontaneously and in a controlled manner during peptide translation. Our new approach generates macrocycles with a more rigid cross-link and with better control of regiochemistry when additional cysteines are present, opening these up for further exploitation in chemical modification of in vitro translated peptides, and so is a valuable addition to the peptide discovery toolbox.", author = "Minglong Liu and Richard Morewood and Ryoji Yoshisada and Pascha, \{Mirte N.\} and Hopstaken, \{Antonius J.P.\} and Eliza Tarcoveanu and Poole, \{David A.\} and \{de Haan\}, \{Cornelis A.M.\} and Christoph Nitsche and Jongkees, \{Seino A.K.\}", note = "Funding Information: CN thanks the Australian Research Council for a Discovery Project (DP230100079) and a Future Fellowship (FT220100010). SJ and RY acknowledge support from the Dutch Research Council grant number OCENW.KLEIN.248, and RY acknowledges further support from the Takenaka Scholarship Foundation. Publisher Copyright: {\textcopyright} 2023 The Royal Society of Chemistry.", year = "2023", doi = "10.1039/d3sc03117a", language = "English", volume = "2023", pages = "10561–10569", journal = "Chemical Science", issn = "2041-6520", publisher = "Royal Society of Chemistry", number = "38", } . Chemical Science.

David A. Poole, III, Eduard O. Bobylev, Bas de Bruin, Simon Mathew, Joost N. H. Reek (2023). Exposing Mechanisms for Defect Clearance in Supramolecular Self-Assembly: Palladium–Pyridine Coordination Revisited . Inorganic Chemistry.

Minglong Liu, Ryoji Yoshisada, Avand Amedi, Antonius J. P. Hopstaken, Mirte N. Pascha, Cornelis A. M. de Haan, Daan P. Geerke, David A. Poole, III, Seino A. K. Jongkees (2023). An Efficient, Site‐Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation . Chemistry – A European Journal.

An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation @article{1737dd4eb9eb41448ca76920dbf5f53f, title = "An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation", abstract = "Macrocyclisation provides a means of stabilising the conformation of peptides, often resulting in improved stability, selectivity, affinity, and cell permeability. In this work, a new approach to peptide macrocyclisation is reported, using a cyanobenzothiazole-containing amino acid that can be incorporated into peptides by both in vitro translation and solid phase peptide synthesis, meaning it should be applicable to peptide discovery by mRNA display. This cyclisation proceeds rapidly, with minimal by-products, is selective over other amino acids including non N-terminal cysteines, and is compatible with further peptide elaboration exploiting such an additional cysteine in bicyclisation and derivatisation reactions. Molecular dynamics simulations show that the new cyclisation group is likely to influence the peptide conformation as compared to previous thioether-based approaches, through rigidity and intramolecular aromatic interactions, illustrating their complementarity.", keywords = "chemoselective reactions, cysteine, in vitro translation, macrocyclisation, peptides", author = "Minglong Liu and Ryoji Yoshisada and Avand Amedi and Hopstaken, \{Antonius J.P.\} and Pascha, \{Mirte N.\} and \{de Haan\}, \{Cornelis A.M.\} and Geerke, \{Daan P.\} and Poole, \{David A.\} and Jongkees, \{Seino A.K.\}", note = "Funding Information: Peptide L4 thioether was previously synthesised by Ir. V Thijssen. We thank Dr. Ir. J A W Kruijtzer of Utrecht University for assistance with initial model peptide synthesis, Dr. S A Neubacher of VU Amsterdam for assistance with CD measurements, and Prof. P E G Leonards and Dr E R Amstalden van Hove for assistance with MALDI measurements. SJ and RY acknowledge support from the Dutch Research Council grant number OCENW.KLEIN.248, and RY acknowledges further support from the Takenaka Scholarship Foundation. MNP and CAMH acknowledge financial support from the One Health Investment Fund from the Faculty of Veterinary Medicine of the Utrecht University. TOC figure generated in part using DALL.E 2. Publisher Copyright: {\textcopyright} 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.", year = "2023", month = mar, day = "7", doi = "10.1002/chem.202203923", language = "English", volume = "29", pages = "1--9", journal = "Chemistry - A European Journal", issn = "0947-6539", publisher = "John Wiley and Sons Inc.", number = "14", } . Chemistry - A European Journal.

Meiling Xu, Bin Sun, David A. Poole, Eduard O. Bobylev, Xu Jing, Jinguo Wu, Cheng He, Chunying Duan, Joost N. H. Reek (2023). Broadening the catalytic region from the cavity to windows by M6L12 nanospheres in cyclizations . Chemical Science.

Eduard O. Bobylev, Renzo A. Knol, Simon Mathew, David A. Poole, Ioli Kotsogianni, Nathaniel I. Martin, Bas de Bruin, Alexander Kros, Joost N. H. Reek (2023). In vivo biodistribution of kinetically stable Pt2L4 nanospheres that show anti-cancer activity . Chemical Science.

Eduard. O. Bobylev, Leonardo Passerini, Felix J. de Zwart, David A. Poole, Simon Mathew, Martina Huber, Bas de Bruin, Joost N. H. Reek (2023). Pd12MnL24 (for n = 6, 8, 12) nanospheres by post-assembly modification of Pd12L24 spheres . Chemical Science.

Minglong Liu, Richard Morewood, Ryoji Yoshisada, Mirte N. Pascha, Antonius J. P. Hopstaken, Eliza Tarcoveanu, David A. Poole, Cornelis A. M. de Haan, Christoph Nitsche, Seino A. K. Jongkees (2023). Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis . Chemical Science.

Pim R. Linnebank, David A. Poole, Alexander M. Kluwer, Joost N. H. Reek (2023). A substrate descriptor based approach for the prediction and understanding of the regioselectivity in caged catalyzed hydroformylation . Faraday Discussions.

Just Add Water: Modulating the Structure-Derived Acidity of Catalytic Hexameric Resorcinarene Capsules @article{4ef6ea319e99408dbe07fe59991d6864, title = "Just Add Water: Modulating the Structure-Derived Acidity of Catalytic Hexameric Resorcinarene Capsules", abstract = "The hexameric undecyl-resorcin[4]arene capsule (C11R6) features eight discrete structural water molecules located at the vertices of its cubic suprastructure. Combining NMR spectroscopy with classical molecular dynamics (MD), we identified and characterized two distinct species of this capsule, C11R6-A and C11R6-B, respectively featuring 8 and 15 water molecules incorporated into their respective hydrogen-bonded networks. Furthermore, we found that the ratio of the C11R6-A and C11R6-B found in solution can be modulated by controlling the water content of the sample. The importance of this supramolecular modulation in C11R6 capsules is highlighted by its ability to perform acid-catalyzed transformations, which is an emergent property arising from the hydrogen bonding within the suprastructure. We show that the conversion of C11R6-A to C11R6-B enhances the catalytic rate of a model Diels-Alder cyclization by 10-fold, demonstrating the cofactor-derived control of a supramolecular catalytic process that emulates natural enzymatic systems.", author = "D.A. Poole and S. Mathew and J.N.H. Reek", year = "2021", month = oct, day = "13", doi = "10.1021/jacs.1c04924", language = "English", volume = "143", pages = "16419--16427", journal = "Journal of the American Chemical Society", issn = "0002-7863", publisher = "American Chemical Society", number = "40", } . Journal of the American Chemical Society.

How to Prepare Kinetically Stable Self-assembled Pt12L24 Nanocages while Circumventing Kinetic Traps @article{0e2361b1170c4a0e9b5c9046484494ab, title = "How to Prepare Kinetically Stable Self-assembled Pt12L24 Nanocages while Circumventing Kinetic Traps", abstract = "{\textcopyright} 2021 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbHSupramolecular coordination-based self-assembled nanostructures have been widely studied, and currently various applications are being explored. For several applications, the stability of the nanostructure is of key importance, and this strongly depends on the metal used in the self-assembly process. Herein, design strategies and synthetic protocols to access desirable kinetically stable Pt12L24 nanospheres are reported, and it is demonstrated that these are stable under conditions under which the palladium counterparts decompose. Descriptors previously used for palladium nanospheres are insufficient for platinum analogues, as the stronger metal–ligand bond results in a mixture of kinetically trapped structures. We report that next to the dihedral angle, the rigidity of the ditopic ligand is also a key parameter for the controlled formation of Pt12L24 nanospheres. Catalytic amounts of coordinating additives to labilise the platinum-pyridyl bond to some extent are needed to selectively form Pt12L24 assemblies. The formed Pt12L24 nanospheres were demonstrated to be stable in the presence of chloride, amines and acids, unlike the palladium analogues.", author = "E.O. Bobylev and D.A. Poole and \{de Bruin\}, B. and J.N.H. Reek", year = "2021", month = sep, day = "1", doi = "10.1002/chem.202101931", language = "English", volume = "27", pages = "12667--12674", journal = "Chemistry - A European Journal", issn = "0947-6539", publisher = "John Wiley and Sons Inc.", number = "49", } . Chemistry - A European Journal.

Selective formation of Pt12L24nanospheres by ligand design @article{411912f393fd40a8a8232aea9c7a636c, title = "Selective formation of Pt12L24nanospheres by ligand design", abstract = "{\textcopyright} The Royal Society of Chemistry 2021.Supramolecular self-assemblies are used across various fields for different applications including their use as containers for catalysts, drugs and fluorophores. M12L24spheres are among the most studied, as they offer plenty of space for functionalization, yielding systems with unique properties in comparison to their single components. Detailed studies on the formation of M12L24structures using palladium cornerstones (that have generally dynamic coordination chemistry) aided in the development of synthetic protocols. The more robust platinum-based systems received thus far much less attention. The general use of platinum-based assemblies remains elusive as parameters and design principles of the ligand building blocks are not fully established. As platinum-based nanospheres are more robust due to the kinetically more stable nitrogen-platinum bond, we studied the sphere formation process in detail in order to develop descriptors for the formation of platinum-based nanospheres. In a systematic study, using time-dependent mass spectrometry,1H-NMR and DOSY NMR, we identified new kinetically trapped intermediates during the formation of Pt12L24spheres and we developed key parameters for selective formation of Pt12L24spheres. Molecular mechanics calculations and experimental result support the importance of charge and steric bulk placed at theendo-site of the ditopic linker for selective sphere formation. Applicability of these principles is demonstrated by employing various ditopic ligands with different bend-angles for the synthesis of a range of Pt2L4, Pt3L6, Pt4L8and Pt12L24polyhedra with platinum cornerstones in excellent yields, thus paving the way for future applications of well-defined robust platinum nanospheres of different shapes and sizes with the general composition PtnL2n", author = "E.O. Bobylev and \{Poole III\}, D.A. and \{de Bruin\}, B. and J.N.H. Reek", year = "2021", month = jun, day = "14", doi = "10.1039/d1sc01295a", language = "English", volume = "12", pages = "7696--7705", journal = "Chemical Science", issn = "2041-6520", publisher = "Royal Society of Chemistry", number = "22", } . Chemical Science.

Topological prediction of palladium coordination cages @article{956b172a72da4e96bfaadb88cc10db71, title = "Topological prediction of palladium coordination cages", abstract = "{\textcopyright} The Royal Society of Chemistry.The preparation of functionalized, heteroleptic PdxL2x coordination cages is desirable for catalytic and optoelectronic applications. Current rational design of these cages uses the angle between metal-binding (∠B) sites of the di(pyridyl)arene linker to predict the topology of homoleptic cages obtained via non-covalent chemistry. However, this model neglects the contributions of steric bulk between the pyridyl residues - a prerequisite for endohedrally functionalized cages, and fails to rationalize heteroleptic cages. We describe a classical mechanics (CM) approach to predict the topological outcomes of PdxL2x coordination cage formation with arbitrary linker combinations, accounting for the electronic effects of coordination and steric effects of linker structure. Initial validation of our CM method with reported homoleptic Pd12LFu24 (LFu = 2,5-bis(pyridyl)furan) assembly suggested the formation of a minor topology Pd15LFu30, identified experimentally by mass spectrometry. Application to heteroleptic cage systems employing mixtures of LFu (∠B = 127°) and its thiophene congener LTh (∠B = 149° ∠Bexp = 152.4°) enabled prediction of Pd12L24 and Pd24L48 coordination cages formation, reliably emulating experimental data. Finally, the topological outcome for exohedrally (LEx) and endohedrally (LEn) functionalized heteroleptic PdxL2x coordination cages were predicted to assess the effect of steric bulk on both topological outcomes and coordination cage yields, with comparisons drawn to experimental data. This journal is", author = "D.A. Poole and E.O. Bobylev and S. Mathew and J.N.H. Reek", year = "2020", month = dec, day = "7", doi = "10.1039/d0sc03992f", language = "English", volume = "11", pages = "12350--12357", journal = "Chemical Science", issn = "2041-6520", publisher = "Royal Society of Chemistry", number = "45", } . Chemical Science.

Balancing Ligand Flexibility versus Rigidity for the Stepwise Self-Assembly of M12L24 via M6L12 Metal–Organic Cages @article{6c4058cafea74f7687756e2728780353, title = "Balancing Ligand Flexibility versus Rigidity for the Stepwise Self-Assembly of M12L24 via M6L12 Metal–Organic Cages", abstract = "{\textcopyright} 2020 Wiley-VCH GmbHNon-covalent interactions are important for directing protein folding across multiple intermediates and can even provide access to multiple stable structures with different properties and functions. Herein, we describe an approach for mimicking this behavior in the self-assembly of metal–organic cages. Two ligands, the bend angles of which are controlled by non-covalent interactions and one ligand lacking the above-mentioned interactions, were synthesized and used for self-assembly with Pd2+. As these weak interactions are easily broken, the bend angles have a controlled flexibility giving access to M2(L1)4, M6(L2)12, and M12(L2)24 cages. By controlling the self-assembly conditions this process can be directed in a stepwise fashion. Additionally, the multiple endohedral hydrogen-bonding sites on the ligand were found to play a role in the binding and discrimination of neutral guests.", author = "C.-L. Liu and E.O. Bobylev and Y. Fu and D.A. Poole and K. Robeyns and C.-A. Fustin and Y. Garcia and J.N.H. Reek and M.L. Singleton", year = "2020", month = sep, day = "16", doi = "10.1002/chem.202001399", language = "English", volume = "26", pages = "11960--11965", journal = "Chemistry - A European Journal", issn = "0947-6539", publisher = "John Wiley and Sons Inc.", number = "52", } . Chemistry - A European Journal.

Protection of Ruthenium Olefin Metathesis Catalysts by Encapsulation in a Self-assembled Resorcinarene Capsule @article{7ce081fc1de14512969c2de13d819350, title = "Protection of Ruthenium Olefin Metathesis Catalysts by Encapsulation in a Self-assembled Resorcinarene Capsule", abstract = "{\textcopyright} 2020 Wiley-VCH Verlag GmbH \& Co. KGaA, WeinheimCatalyst encapsulation is examined as a means of increasing the productivity of olefin metathesis catalysts. Commercially available, cationic ruthenium metathesis catalysts were incorporated into a supramolecular resorcin[4]arene capsule. Encapsulation increased catalyst stability in water-saturated toluene, delivering higher metathesis yields than the parent, non-encapsulated Hoveyda catalyst in the same reaction medium.", author = "L.J. Jongkind and M. Rahimi and D. Poole and S.J. Ton and D.E. Fogg and J.N.H. Reek", year = "2020", month = aug, day = "20", doi = "10.1002/cctc.202000111", language = "English", volume = "12", pages = "4019--4023", journal = "ChemCatChem", issn = "1867-3880", publisher = "Wiley - VCH Verlag GmbH \& CO. KGaA", number = "16", } . ChemCatChem.

Control over Electrochemical Water Oxidation Catalysis by Preorganization of Molecular Ruthenium Catalysts in Self-Assembled Nanospheres @article{75c2cd1c18014a479e9879902c362fce, title = "Control over Electrochemical Water Oxidation Catalysis by Preorganization of Molecular Ruthenium Catalysts in Self-Assembled Nanospheres", abstract = "{\textcopyright} 2018 The Authors. Published by Wiley-VCH Verlag GmbH \& Co. KGaA.Oxygen formation through water oxidation catalysis is a key reaction in the context of fuel generation from renewable energies. The number of homogeneous catalysts that catalyze water oxidation at high rate with low overpotential is limited. Ruthenium complexes can be particularly active, especially if they facilitate a dinuclear pathway for oxygen bond formation step. A supramolecular encapsulation strategy is reported that involves preorganization of dilute solutions (10−5 m) of ruthenium complexes to yield high local catalyst concentrations (up to 0.54 m). The preorganization strategy enhances the water oxidation rate by two-orders of magnitude to 125 s−1, as it facilitates the diffusion-controlled rate-limiting dinuclear coupling step. Moreover, it modulates reaction rates, enabling comprehensive elucidation of electrocatalytic reaction mechanisms.", author = "F. Yu and D. Poole and S. Mathew and N. Yan and J. Hessels and N. Orth and I. Ivanovi{\'c}-Burmazovi{\'c} and J.N.H. Reek", year = "2018", month = aug, day = "27", doi = "10.1002/anie.201805244", language = "English", volume = "57", pages = "11247--11251", journal = "Angewandte Chemie - International Edition", issn = "1433-7851", publisher = "John Wiley and Sons Ltd", number = "35", } . Angewandte Chemie - International Edition.