Computational insights into aqueous speciation of metal-oxide nanoclusters: an in-depth study of the Keggin phosphomolybdate.

Herein, we present a new computational methodology that unlocks the prediction of the complex multi-species multi-equilibria processes involved in the formation of complex metal-oxo nanoclusters. Relying on our recently introduced method named POMSimulator, we extended its capabilities and challenged its accuracy with the well-known phosphomolybdate [PMo12O40]3- Keggin anion system. We show how the use of statistical techniques enabled the processing of a vast number of speciation models and their associated systems of non-linear equations efficiently and in a scalable manner. Subsequently, this approach is applied to generate statistically averaged speciation diagrams and their associated error bars. Then, we unveil the previously unreported speciation phase diagram under varying [Mo]/[P] ratios vs. pH. Our findings align well with experimental data, indicating the prevalence of the Keggin {PMo12} as the primary species at low pH, but the lacunary {PMo11}and Strandberg {P2Mo5} anions also emerge as major species at other concentration ratios. Finally, from 7 × 104 speciation models we inferred a plausible reaction network across the diverse nuclearities present within the system, which underlines the role of trimers as key intermediate building blocks.

Supramolecular Anchoring of Fe(III) Molecular Redox Catalysts into Graphitic Surfaces Via CH-π and π-π Interactions for CO2 Electroreduction.

Photoelectrochemical devices require solid anodes and cathodes for the easy assembling of the whole cell and thus redox catalysts need to be deposited on the electrodes. Typical catalyst deposition involves drop casting, spin coating, doctor blading or related techniques to generate modified electrodes where the active catalyst in contact with the electrolyte is only a very small fraction of the deposited mass. We have developed a methodology where the redox catalyst is deposited at the electrode based on supramolecular interactions, namely CH-π and π-π between the catalyst and the surface. This generates a very well-defined catalysts-surface structure and electroactivity, together with a very large catalytic response. This approach represents a new anchoring strategy that can be applied to catalytic redox reactions in heterogeneous phase and compared to traditional methods involves about 4-5 orders of magnitude less mass deposition to achieve comparable activity and with very well-behaved electroactivity and stability.

POMSimulator: An open-source tool for predicting the aqueous speciation and self-assembly mechanisms of polyoxometalates.

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.

Bicyclic Guanidine Promoted Mechanistically Divergent Depolymerization and Recycling of a Biobased Polycarbonate.

We here report the organocatalytic and temperature-controlled depolymerization of biobased poly(limonene carbonate) providing access to its trans-configured cyclic carbonate as the major product. The base TBD (1,5,7-triazabicyclo[4.4.0]dec-5-ene) offers a unique opportunity to break down polycarbonates via end-group activation or main chain scission pathways as supported by various controls and computational analysis. These energetically competitive processes represent an unprecedented divergent approach to polycarbonate recycling. The trans limonene carbonate can be converted back to its polycarbonate via ring-opening polymerization using the same organocatalyst in the presence of an alcohol initiator, offering thus a potential circular and practical route for polycarbonate recycling.

Multi-Time-Scale Simulation of Complex Reactive Mixtures: How Do Polyoxometalates Form?

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.

A redox-active inorganic crown ether based on a polyoxometalate capsule.

Cation-uptake has been long researched as an important topic in materials science. Herein we focus on a molecular crystal composed of a charge-neutral polyoxometalate (POM) capsule [MoVI72FeIII30O252(H2O)102(CH3CO2)15]3+ encapsulating a Keggin-type phosphododecamolybdate anion [α-PMoVI12O40]3-. Cation-coupled electron-transfer reaction occurs by treating the molecular crystal in an aqueous solution containing CsCl and ascorbic acid as a reducing reagent. Specifically, multiple Cs+ ions and electrons are captured in crown-ether-like pores {MoVI3FeIII3O6}, which exist on the surface of the POM capsule, and Mo atoms, respectively. The locations of Cs+ ions and electrons are revealed by single-crystal X-ray diffraction and density functional theory studies. Highly selective Cs+ ion uptake is observed from an aqueous solution containing various alkali metal ions. Cs+ ions can be released from the crown-ether-like pores by the addition of aqueous chlorine as an oxidizing reagent. These results show that the POM capsule functions as an unprecedented "redox-active inorganic crown ether", clearly distinguished from the non-redox-active organic counterpart.

A new series of bioactive Mo(V)2O2S2-based thiosemicarbazone complexes: Solution and DFT studies, and antifungal and antioxidant activities.

This paper deals with the synthesis, characterization, and studies of biological properties of a series of 5 coordination compounds based on binuclear core [Mo(V)2O2S2]2+ with thiosemicarbazones ligands bearing different substituents on the R1 position of the ligand. The complexes are first studied using MALDI-TOF mass spectrometry and NMR spectroscopy to determine their structures in solution in relation to single-crystal X-Ray diffraction data. In a second part, the antifungal and antioxidative activities are explored and the high potential of these coordination compounds compared to the uncoordinated ligands is demonstrated for these properties. Finally, DFT calculation provides important support to the solution studies by identifying the most stable isomers in each [Mo2O2S2]2+/Ligand system, while the determination of HUMO and LUMO levels is performed to explain the antioxidative properties of these systems.

Grafting of Anionic Decahydro-Closo-Decaborate Clusters on Keggin and Dawson-Type Polyoxometalates: Syntheses, Studies in Solution, DFT Calculations and Electrochemical Properties.

Herein we report the synthesis of a new class of compounds associating Keggin and Dawson-type Polyoxometalates (POMs) with a derivative of the anionic decahydro-closo-decaborate cluster [B10H10]2- through aminopropylsilyl ligand (APTES) acting as both a linker and a spacer between the two negatively charged species. Three new adducts were isolated and fully characterized by various NMR techniques and MALDI-TOF mass spectrometry, notably revealing the isolation of an unprecedented monofunctionalized SiW10 derivative stabilized through intramolecular H-H dihydrogen contacts. DFT as well as electrochemical studies allowed studying the electronic effect of grafting the decaborate cluster on the POM moiety and its consequences on the hydrogen evolution reaction (HER) properties.

Computational Prediction of Speciation Diagrams and Nucleation Mechanisms: Molecular Vanadium, Niobium, and Tantalum Oxide Nanoclusters in Solution.

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.

Mechanistic insights of molecular metal polyselenides for catalytic hydrogen generation.

Molecular metal chalcogenides have attracted great attention as electrocatalysts for the hydrogen evolution reaction (HER). However, efficient utilisation of the active sites and catalytic performance modulation has been challenging. Here we explore the design of immobilized molecular molybdenum polyselenides [Mo2O2S2(Se2)(Sex)]2- that exhibit efficient hydrogen evolution at low overpotential and stability over 1000 cycles. Density functional calculations provide evidence of a unimolecular mechanism in the HER process via the exploration of viable reaction pathways. The discussed findings are of a broad interest in the development of efficient molecular electrocatalytic materials.

Unparalleled selectivity and electronic structure of heterometallic [LnLn'Ln] molecules as 3-qubit quantum gates.

Heterometallic lanthanide [LnLn'] coordination complexes that are accessible thermodynamically are very scarce because the metals of this series have very similar chemical behaviour. Trinuclear systems of this category have not been reported. A coordination chemistry scaffold has been shown to produce molecules of type [LnLn'Ln] of high purity, i.e. exhibiting high metal distribution ability, based on their differences in ionic radius. Through a detailed analysis of density functional theory (DFT) based calculations, we discern the energy contributions that lead to the unparalleled chemical selectivity of this molecular system. Some of the previously reported examples are compared here with the newly prepared member of this exotic list, [Er2Pr(LA)2(LB)2(py)(H2O)2](NO3) (1) (H2LA and H2LB are two ß-diketone ligands). A magnetic analysis extracted from magnetization and calorimetry determinations identifies the necessary attributes for it to act as an addressable, conditional multiqubit spin-based quantum gate. Complementary ab initio calculations confirm the feasibility of these complexes as composite quantum gates, since they present well-isolated ground states with highly anisotropic and distinct g-tensors. The electronic structure of 1 has also been analyzed by EPR. Pulsed experiments have allowed the establishment of the quantum coherence of the transitions within the relevant spin states, as well as the feasibility of a coherent control of these states via nutation experiments.

Chemical reaction network knowledge graphs: the OntoRXN ontology.

The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities on a certain field and how these entities are interrelated. In this work, we introduce OntoRXN, a novel ontology describing the reaction networks constructed from computational chemistry calculations. Under our paradigm, these networks are handled as undirected graphs, without assuming any traversal direction. From there, we propose a core class structure including reaction steps, network stages, chemical species, and the lower-level entities for the individual computational calculations. These individual calculations are founded on the OntoCompChem ontology and on the ioChem-BD database, where information is parsed and stored in CML format. OntoRXN is introduced through several examples in which knowledge graphs based on the ontology are generated for different chemical systems available on ioChem-BD. Finally, the resulting knowledge graphs are explored through SPARQL queries, illustrating the power of the semantic approach to standardize the analysis of intricate datasets and to simplify the development of complex workflows.

Elucidating Sulfide Activation Mode in Metal-Catalyzed Sulfoxidation Reactivity.

Interest in the catalytic activation of peroxides, together with the requirement of stereoselectivity for the production of enantiopure sulfoxides, has made sulfoxidation the ideal playground for theoretical and experimental physical organic chemists investigating oxidation reactivity. Efforts have been dedicated for elucidating the catalytic pathway regarding these species and for dissecting out the dominant factors influencing the yield and stereochemistry. In this article, Ti(IV) and Hf(IV) aminotriphenolate complexes have been prepared and investigated as catalysts in the presence of peroxides in sulfide oxidation. Experimental results have been combined with theoretical calculations obtaining detailed mechanistic information on oxygen transfer processes. The study revealed that steric issues are mainly responsible for the formation of intermediates in the oxidation pathway. In particular, we could highlight the occurrence of a blended situation where the steric effects of sulfides, ligands, and oxidants influence the formation of different intermediates and reaction pathways.

Predicting the Solubility of Inorganic Ion Pairs in Water.

Polyoxometalates (POMs), ranging in size from 1 to 10's of nanometers, resemble building blocks of inorganic materials. Elucidating their complex solubility behavior with alkali-counterions can inform natural and synthetic aqueous processes. In the study of POMs ([Nb24 O72 H9 ]15- , Nb24 ) we discovered an unusual solubility trend (termed anomalous solubility) of alkali-POMs, in which Nb24 is most soluble with the smallest (Li+ ) and largest (Rb/Cs+ ) alkalis, and least soluble with Na/K+ . Via computation, we define a descriptor (σ-profile) and use an artificial neural network (ANN) to predict all three described alkali-anion solubility trends: amphoteric, normal (Li+ >Na+ >K+ >Rb+ >Cs+ ), and anomalous (Cs+ >Rb+ >K+ >Na+ >Li+ ). Testing predicted amphoteric solubility affirmed the accuracy of the descriptor, provided solution-phase snapshots of alkali-POM interactions, yielded a new POM formulated [Ti6 Nb14 O54 ]14- , and provides guidelines to exploit alkali-POM interactions for new POMs discovery.

Ni-Catalyzed Decarboxylative Silylation of Alkynyl Carbonates: Access to Chiral Allenes via Enantiospecific Conversions.

A Ni-mediated decarboxylative silylation of alkynyl cyclic carbonates used as versatile propargylic surrogates is reported affording a wide range of highly substituted 2,3- and 3,4-allenol products in good yields. The formal cross-coupling between a tentative intermediate Ni(allenyl) and the silyl reagent was further extended to enantiospecific conversions providing access to chiral allene synthons. This protocol marks the first Ni-catalyzed propargylic silylation proceeding through an SN2' manifold.

New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited.

The level of detail attained in the computational description of reaction mechanisms can be vastly improved through tools for automated chemical space exploration, particularly for systems of small to medium size. Under this approach, the unimolecular decomposition landscape for indole was explored through the automated reaction mechanism discovery program AutoMeKin. Nevertheless, the sheer complexity of the obtained mechanisms might be a hindrance regarding their chemical interpretation. In this spirit, the new Python library amk-tools has been designed to read and manipulate complex reaction networks, greatly simplifying their overall analysis. The package provides interactive dashboards featuring visualizations of the network, the three-dimensional (3D) molecular structures and vibrational normal modes of all chemical species, and the corresponding energy profiles for selected pathways. The combination of the joined mechanism generation and postprocessing workflow with the rich chemistry of indole decomposition enabled us to find new details of the reaction (obtained at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level of theory) that were not reported before: (i) 16 pathways leading to the formation of HCN and NH3 (via amino radical); (ii) a barrierless reaction between methylene radical and phenyl isocyanide, which might be an operative mechanism under the conditions of the interstellar medium; and (iii) reaction channels leading to both hydrogen cyanide and hydrogen isocyanide, of potential astrochemical interest as the computed HNC/HCN ratios greatly exceed the calculated equilibrium value at very low temperatures. The reported reaction networks can be very valuable to supplement databases of kinetic data, which is of remarkable interest for pyrolysis and astrochemical studies.

Rationalizing the Mechanism of Peroxyformate Decomposition: Computational Insights To Understand Solvent Influence.

The heterolytic decomposition of tert-butyl peroxyformate to tert-butanol and carbon dioxide, catalyzed by pyridine, is a long-known example of a reaction whose kinetics are strongly affected by solvent polarity. From DFT and ab initio methods together with the SMD implicit solvation model, an extension on the formerly accepted mechanism is proposed. This novel proposal involves the formation of a carbonic acid ester intermediate and its further decomposition, through an unreported pyridine-mediated stepwise route. Computed barriers for this mechanism at DLPNO/CCSD(T)-def2-TZVP are in excellent agreement with experimental kinetic data across different solvents. Furthermore, the strong relationships between activation energies, geometric parameters in the transition state and the characteristics of the different solvents are also analyzed in depth.

Unlocking Phase Diagrams for Molybdenum and Tungsten Nanoclusters and Prediction of their Formation Constants.

Understanding and controlling aqueous speciation of metal oxides are key for the discovery and development of novel materials, and challenge both experimental and computational approaches. Here we present a computational method, called POMSimulator, which is able to predict speciation phase diagrams (Conc. vs pH) for multispecies chemical equilibria in solution, and which we apply to molybdenum and tungsten isopolyoxoanions (IPAs). Starting from the MO4 monomers, and considering dimers, trimers, and larger species, the chemical reaction networks involved in the formation of [H32Mo36O128]8- and [W12O42]12- are sampled in an automatic manner. This information is used for setting up ∼105 speciation models, and from there, we generate the speciation phase diagrams, which show an insightful picture of the behavior of IPAs in aqueous solution. Furthermore, we predict the values of 107 formation constants for a diversity of molybdenum and tungsten molecular oxides. Among these species, we could include several pentagonal-shaped species and very reactive tungsten intermediates as well. Last but not least, the calibration employed for correcting the density functional theory (DFT) Gibbs energies is remarkably similar for both metals, which suggests that a general rule might exist for correcting computed free energies for other metals.

Testing automatic methods to predict free binding energy of host-guest complexes in SAMPL7 challenge.

The design of new host-guest complexes represents a fundamental challenge in supramolecular chemistry. At the same time, it opens new opportunities in material sciences or biotechnological applications. A computational tool capable of automatically predicting the binding free energy of any host-guest complex would be a great aid in the design of new host systems, or to identify new guest molecules for a given host. We aim to build such a platform and have used the SAMPL7 challenge to test several methods and design a specific computational pipeline. Predictions will be based on machine learning (when previous knowledge is available) or a physics-based method (otherwise). The formerly delivered predictions with an RMSE of 1.67 kcal/mol but will require further work to identify when a specific system is outside of the scope of the model. The latter is combines the semiempirical GFN2B functional, with docking, molecular mechanics, and molecular dynamics. Correct predictions (RMSE of 1.45 kcal/mol) are contingent on the identification of the correct binding mode, which can be very challenging for host-guest systems with a large number of degrees of freedom. Participation in the blind SAMPL7 challenge provided fundamental direction to the project. More advanced versions of the pipeline will be tested against future SAMPL challenges.

Unveiling a Photoinduced Hydrogen Evolution Reaction Mechanism via the Concerted Formation of Uranyl Peroxide.

We present a density functional theory study for the photochemical water oxidation reaction promoted by uranyl nitrate upon sunlight radiation. First, we explored the most stable uranyl complex in the absence of light. The reaction in a dark environmen proceeds through the condensation of uranyl monomers to form dimeric hydroxo-bridged species, which is the first step toward a hydrogen evolution reaction (HER). We found a triplet-state-driven mechanism that leads to the formation of uranyl peroxide and hydrogen gas. To describe in detail this reaction path, we characterized the singlet and triplet low-lying states of the dimeric hydroxo-bridged species, including minima, transition states, minimal energy crossing points, and adiabatic energies. Our computational results provide mechanistic insights that are in good agreement with the experimental data available.