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Petrus E, Buils J, Garay-Ruiz D, Segado-Centellas M, Bo C. POMSimulator: An open-source tool for predicting the aqueous speciation and self-assembly mechanisms of polyoxometalates. J Comput Chem 2024; 45:2242-2250. [PMID: 38826122 DOI: 10.1002/jcc.27389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 06/04/2024]
Abstract
Elucidating the speciation (in terms of concentration versus pH) and understanding the formation mechanisms of polyoxometalates remains a significant challenge, both in experimental and computational domains. POMSimulator is a new methodology that tackles this problem from a purely computational perspective. The methodology uses results from quantum mechanics based methods to automatically set up the chemical reaction network, and to build speciation models. As a result, it becomes possible to predict speciation and phase diagrams, as well as to derive new insights into the formation mechanisms of large molecular clusters. In this work we present the main features of the first open-source version of the software. Since the first report [Chem. Sci. 2020, 11, 8448-8456], POMSimulator has undergone several improvements to keep up with the growing challenges that were tackled. After four years of research, we recognize that the source code is sufficiently stable to share a polished and user-friendly version. The Python code, manual, examples, and install instructions can be found at https://github.com/petrusen/pomsimulator.
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Affiliation(s)
- Enric Petrus
- Department of Environmental Chemistry, EAWAG: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jordi Buils
- Institute of Chemical Research of Catalonia (ICIQ), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Diego Garay-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ), Tarragona, Spain
| | - Mireia Segado-Centellas
- Institute of Chemical Research of Catalonia (ICIQ), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
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Malcolm D, Vilà-Nadal L. Computational Study into the Effects of Countercations on the [P 8W 48O 184] 40- Polyoxometalate Wheel. ACS ORGANIC & INORGANIC AU 2023; 3:274-282. [PMID: 37810411 PMCID: PMC10557121 DOI: 10.1021/acsorginorgau.3c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 10/10/2023]
Abstract
Porous metal oxide materials have been obtained from a ring-shaped macrocyclic polyoxometalate (POM) structural building unit, [P8W48O184]40-. This is a tungsten oxide building block with an integrated "pore" of 1 nm in diameter, which, when connected with transition metal linkers, can assemble frameworks across a range of dimensions and which are generally referred to as POMzites. Our investigation proposes to gain a better understanding into the basic chemistry of this POM, specifically local electron densities and locations of countercations within and without the aforementioned pore. Through a rigorous benchmarking process, we discovered that 8 potassium cations, located within the pore, provided us with the most accurate model in terms of mimicking empirical properties to a sufficient degree of accuracy while also requiring a relatively small number of computer cores and hours to successfully complete a calculation. Additionally, we analyzed two other similar POMs from the literature, [As8W48O184]40- and [Se8W48O176]32-, in the hopes of determining whether they could be similarly incorporated into a POMzite network; given their close semblance in terms of local electron densities and interaction with potassium cations, we judge these POMs to be theoretically suitable as POMzite building blocks. Finally, we experimented with substituting different cations into the [P8W48O184]40- pore to observe the effect on pore dimensions and overall reactivity; we observed that the monocationic structures, particularly the Li8[P8W48O184]32- framework, yielded the least polarized structures. This correlates with the literature, validating our methodology for determining general POM characteristics and properties moving forward.
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Affiliation(s)
- Daniel Malcolm
- School
of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Laia Vilà-Nadal
- School
of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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Petrus E, Garay-Ruiz D, Reiher M, Bo C. Multi-Time-Scale Simulation of Complex Reactive Mixtures: How Do Polyoxometalates Form? J Am Chem Soc 2023; 145:18920-18930. [PMID: 37496164 DOI: 10.1021/jacs.3c05514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Understanding the dynamics of reactive mixtures still challenges both experiments and theory. A relevant example can be found in the chemistry of molecular metal-oxide nanoclusters, also known as polyoxometalates. The high number of species potentially involved, the interconnectivity of the reaction network, and the precise control of the pH and concentrations needed in the synthesis of such species make the theoretical/computational treatment of such processes cumbersome. This work addresses this issue relying on a unique combination of recently developed computational methods that tackle the construction, kinetic simulation, and analysis of complex chemical reaction networks. By using the Bell-Evans-Polanyi approximation for estimating activation energies, and an accurate and robust linear scaling for correcting the computed pKa values, we report herein multi-time-scale kinetic simulations for the self-assembly processes of polyoxotungstates that comprise 22 orders of magnitude, from tens of femtoseconds to months of reaction time. This very large time span was required to reproduce very fast processes such as the acid/base equilibria (at 10-12 s), relatively slow reactions such as the formation of key clusters such as the metatungstate (at 103 s), and the very slow assembly of the decatungstate (at 106 s). Analysis of the kinetic data and of the reaction network topology shed light onto the details of the main reaction mechanisms, which explains the origin of kinetic and thermodynamic control followed by the reaction. Simulations at alkaline pH fully reproduce experimental evidence since clusters do not form under those conditions.
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Affiliation(s)
- Enric Petrus
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Avenida Països Catalans, 16, Tarragona 43007, Spain
| | - Diego Garay-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Avenida Països Catalans, 16, Tarragona 43007, Spain
| | - Markus Reiher
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich 8093, Switzerland
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Avenida Països Catalans, 16, Tarragona 43007, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel•li Domingo s/n, Tarragona 43007, Spain
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Gumerova NI, Rompel A. Speciation atlas of polyoxometalates in aqueous solutions. SCIENCE ADVANCES 2023; 9:eadi0814. [PMID: 37343109 DOI: 10.1126/sciadv.adi0814] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
Speciation is the key parameter in solution chemistry that describes the composition, concentration, and oxidation state of each chemical form of an element present in a sample. The speciation study of complex polyatomic ions has remained challenging because of the large number of factors affecting stability and the limited number of direct methods. To address these challenges, we developed the speciation atlas of 10 polyoxometalates commonly used in catalytic and biological applications in aqueous solutions, where the speciation atlas provides both a species distribution database and a predictive model for other polyoxometalates to be used. Compiled for six different polyoxometalate archetypes with three types of addenda ions based on 1309 nuclear magnetic resonance spectra under 54 different conditions, the atlas has revealed a previously unknown behavior of polyoxometalates that may account for their potency as biological agents and catalysts. The atlas is intended to promote the interdisciplinary use of metal oxides in various scientific fields.
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Affiliation(s)
- Nadiia I Gumerova
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Josef-Holaubek-Platz 2, 1090 Wien, Austria
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Josef-Holaubek-Platz 2, 1090 Wien, Austria
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Petrus E, Segado-Centellas M, Bo C. Computational Prediction of Speciation Diagrams and Nucleation Mechanisms: Molecular Vanadium, Niobium, and Tantalum Oxide Nanoclusters in Solution. Inorg Chem 2022; 61:13708-13718. [PMID: 35998382 DOI: 10.1021/acs.inorgchem.2c00925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the aqueous speciation of molecular metal-oxo-clusters plays a key role in different fields such as catalysis, electrochemistry, nuclear waste recycling, and biochemistry. To describe the speciation accurately, it is essential to elucidate the underlying self-assembly processes. Herein, we apply a computational method to predict the speciation and formation mechanisms of polyoxovanadates, -niobates, and -tantalates. While polyoxovanadates have been widely studied, polyoxoniobates and -tantalates lack the same level of understanding. First, we propose a pentavanadate cluster ([V5O14]3-) as a key intermediate for the formation of the decavanadate. Our computed phase speciation diagram is in particularly good agreement with the experiments. Second, we report the formation constants of the heptaniobate, [Nb7O22]9-, decaniobate, [Nb10O28]6-, and tetracosaniobate [H9Nb24O72]15-. Additionally, we compute the speciation and phase diagram of niobium, which so far was restricted to Lindqvist derivates. Finally, we predict the formation constant of the decatantalate ([Ta10O26]6-) in water, even though it had only been synthesized in toluene. Furthermore, we also calculate the corresponding speciation and phase diagrams for polyoxotantalates. Overall, we show that our method can be successfully applied to different families of molecular metal oxides without any need for readjustments; therefore, it can be regarded as a trustworthy tool for exploring polyoxometalates' chemistry.
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Affiliation(s)
- Enric Petrus
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans, 16, 43007 Tarragona, Spain.,Departament de Química Física i Inorgánica, Universitat Rovira i Virgili, Marcel•lí Domingo s/n, 43007 Tarragona, Spain
| | - Mireia Segado-Centellas
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans, 16, 43007 Tarragona, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans, 16, 43007 Tarragona, Spain.,Departament de Química Física i Inorgánica, Universitat Rovira i Virgili, Marcel•lí Domingo s/n, 43007 Tarragona, Spain
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Kondinski A, Rasmussen M, Mangelsen S, Pienack N, Simjanoski V, Näther C, Stares DL, Schalley CA, Bensch W. Composition-driven archetype dynamics in polyoxovanadates. Chem Sci 2022; 13:6397-6412. [PMID: 35733899 PMCID: PMC9159092 DOI: 10.1039/d2sc01004f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022] Open
Abstract
Molecular metal oxides often adopt common structural frameworks (i.e. archetypes), many of them boasting impressive structural robustness and stability. However, the ability to adapt and to undergo transformations between different structural archetypes is a desirable material design feature offering applicability in different environments. Using systems thinking approach that integrates synthetic, analytical and computational techniques, we explore the transformations governing the chemistry of polyoxovanadates (POVs) constructed of arsenate and vanadate building units. The water-soluble salt of the low nuclearity polyanion [V6As8O26]4− can be effectively used for the synthesis of the larger spherical (i.e. kegginoidal) mixed-valent [V12As8O40]4− precipitate, while the novel [V10As12O40]8− POVs having tubular cyclic structures are another, well soluble product. Surprisingly, in contrast to the common observation that high-nuclearity polyoxometalate (POM) clusters are fragmented to form smaller moieties in solution, the low nuclearity [V6As8O26]4− anion is in situ transformed into the higher nuclearity cluster anions. The obtained products support a conceptually new model that is outlined in this article and that describes a continuous evolution between spherical and cyclic POV assemblies. This new model represents a milestone on the way to rational and designable POV self-assemblies. Systems-based elucidation of the polyoxovanadate speciation reveals that heterogroup substitution can transform spherical kegginoids into tubular architectures in a programmable manner.![]()
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Affiliation(s)
- Aleksandar Kondinski
- Department of Chemical Engineering and Biotechnology, University of Cambridge Philippa Fawcett Drive S CB3 0AS UK
| | - Maren Rasmussen
- Institut für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel 24118 Kiel Germany
| | - Sebastian Mangelsen
- Institut für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel 24118 Kiel Germany
| | - Nicole Pienack
- Institut für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel 24118 Kiel Germany
| | - Viktor Simjanoski
- Primer affiliate of University of Chicago Master Program Chicago IL USA
| | - Christian Näther
- Institut für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel 24118 Kiel Germany
| | - Daniel L Stares
- Institut für Chemie und Biochemie der Freien Universität Berlin Arnimallee 20 14195 Berlin Germany
| | - Christoph A Schalley
- Institut für Chemie und Biochemie der Freien Universität Berlin Arnimallee 20 14195 Berlin Germany
| | - Wolfgang Bensch
- Institut für Anorganische Chemie, Christian-Albrechts-Universität zu Kiel 24118 Kiel Germany
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