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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Performance of group additivity methods for predicting the stability of uranyl complexes.

Herein, we investigated the viability of two group additivity methods for predicting Gibbs energies of a set of uranyl complexes. In first place, we proved that both density functional theory (DFT)-based methods and Serezhkin's stereoatomic model provide equivalent answers in terms of stability. Moreover, we proposed a novel methodology based on Mayer's population analysis for estimating Serezhkin's empirical parameters theoretically. On the other hand, we showed that Cheong and Persson linear algebra methodology can be successfully applied to uranyl complexes, and analyzed its performance in connection with the chemical nature of the compounds employed in the model.

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.

Organocatalytic Trapping of Elusive Carbon Dioxide Based Heterocycles by a Kinetically Controlled Cascade Process.

A conceptually novel approach is described for the synthesis of six-membered cyclic carbonates derived from carbon dioxide. The approach utilizes homoallylic precursors that are converted into five-membered cyclic carbonates having a ß-positioned alcohol group in one of the ring substituents. The activation of the pendent alcohol group through an N-heterocyclic base allows equilibration towards a thermodynamically disfavored six-membered carbonate analogue that can be trapped by an acylating agent. Various control experiments and computational analysis of this manifold are in line with a process that is primarily dictated by a kinetically controlled acylation step. This cascade process delivers an ample diversity of six-membered cyclic carbonates in excellent yields and chemoselectivities under mild reaction conditions.

Strategic Capture of the {Nb7 } Polyoxometalate.

Group V Nb-polyoxometalate (Nb-POM) chemistry generally lacks the elegant pH-controlled speciation exhibited by group VI (Mo, W) POM chemistry. Here three Nb-POM clusters were isolated and structurally characterized; [Nb14 O40 (O2 )2 H3 ]14- , [((UO2 )(H2 O))3 Nb46 (UO2 )2 O136 H8 (H2 O)4 ]24- , and [(Nb7 O22 H2 )4 (UO2 )7 (H2 O)6 ]22- , that effectively capture the aqueous Nb-POM species from pH 7 to pH 10. These Nb-POMs illustrate a reaction pathway for control over speciation that is driven by counter-cations (Li+ ) rather than pH. The two reported heterometallic POMs (with UO2 2+ moieties) are stabilized by replacing labile H2 O/HO-Nb=O with very stable O=U=O. The third isolated Nb-POM features cis-yl-oxos, prior observed only in group VI POM chemistry. Moreover, with these actinide-heterometal contributions to the burgeoning Nb-POM family, it now transects all major metal groups of the periodic table.

Alkali-Driven Disassembly and Reassembly of Molecular Niobium Oxide in Water.

Counterions are deemed "spectators" in aqueous solutions of cationic or anionic molecular metal-oxo clusters. While pH and concentration drive aqueous metal speciation as a first approximation, the important effect of counterions is usually overlooked and never considered in standard Pourbaix databases. Alkali counterions for polyoxometalate (POM) clusters control solubility with distinct periodic trends, but evidence for alkali control over speciation is ambiguous. Here we show that a simple Nb-POM, [Nb10O28]6- ({Nb10}), converts to oligomers of (H xNb24O72)(24- x)- ({Nb24}) upon adding only alkali chloride salts, even in buffered neutral solutions. Raman and X-ray scattering reveal that the rate of {Nb10} to {Nb24} conversion increases with alkali cation radius and cation concentration. Cation-bridged oligomers of {Nb24} y ( y = 2,4) are defined by comparing experimental to computed small-angle X-ray scattering spectra. Computational studies and mass spectrometry indicate that the alkalis open the compact {Nb10} cluster in conjunction with protonation of a heptamer {Nb7} intermediate, in which alkali-{Nb10} association at key locations on the cluster initiates the reaction. Computation also explains the alkali periodic trend for {Nb10} to {Nb24} conversion; larger alkalis more effectively destabilize {Nb10}. This periodic trend asserts the hypothesis that Nb-cluster speciation near neutral pH is driven by the alkali cations in the absence of added base or acid. The extremely high solubility of these 3.5 nm polyoxoanion assemblies-2 M Nb at near neutral pH-is both surprising and exploitable for aqueous synthesis of niobate thin films or nanomaterials used in energy and microelectronics applications.

Selective Lanthanide Distribution within a Comprehensive Series of Heterometallic [LnPr] Complexes.

The preparation of heterometallic, lanthanide-only complexes is an extremely difficult synthetic challenge. By a ligand-based strategy, a complete isostructural series of dinuclear heterometallic [LnPr] complexes has been synthesized and structurally characterized. The two different coordination sites featured in this molecular entity allow study of the preferences of the praseodymium ion for a specific position depending on the ionic radii of the accompanying lanthanide partner. The purity of each heterometallic moiety has been evaluated in the solid state and in solution by means of crystallographic and spectrometric methods, respectively, revealing the limits of this strategy for ions with similar sizes. DFT calculations have been carried out to support the experimental results, confirming the nature of the site-selective lanthanide distribution. The predictable selectivity of this system has been exploited to assess the magnetic properties of the [DyPr] and [LuPr] derivatives, showing that the origin of the slow dynamics observed in the former arises from the dysprosium ion.

Electronic Structure Studies on the Whole Keplerate Family: Predicting New Members.

A comprehensive study of the electronic structure of nanoscale molecular oxide capsules of the type [{MVI (MVI )5 O21 }12 {M'V2 O2 (µ-X)(µ-Y)(Ln- )}30 ](12+n)- is presented, where M,M'=Mo,W, and the bridging ligands X,Y=O,S, carried out by means of density functional theory. Discussion of the electronic structure of these derivatives is focused on the thermodynamic stability of each of the structures, the one having the highest HOMO-LUMO gap being M=W, M'=Mo, X=Y=S. For the most well-known structure M=M'=Mo, X=Y=O, [Mo132 O372 ]12- , the chemical bonding of several ligands to the {MoV2 O2 (µ-O)2 } linker moiety produces negligible effects on its stability, which is evidence of a strong ionic component in these bonds. The existence of a hitherto unknown species, namely W132 with both bridging alternatives, is discussed and put into context.

Thermodynamic Stability of Heterodimetallic [LnLn'] Complexes: Synthesis and DFT Studies.

The solid-state and solution configurations of the heterodimetallic complexes (Hpy)[LaEr(HL)3 (NO3 )(py)(H2 O)] (1), (Hpy)[CeEr(HL)3 (NO3 )(py)(H2 O)] (2), (Hpy)[CeGd(HL)3 (NO3 )(py)(H2 O)] (3), (Hpy)[PrSm(HL)3 (NO3 )(py)(H2 O)] (4), and (Hpy)2 [LaYb(HL)3 (NO3 )(H2 O)](NO3 ) (5), in which H3 L is 6-(3-oxo-3-(2-hydroxyphenyl)propionyl)pyridine-2-carboxylic acid and py is pyridine, were analyzed experimentally and by using DFT calculations. Complexes 3, 4, and 5 are described here for the first time, and were analyzed by using single-crystal X-ray diffraction and mass spectrometry. The theoretical study was also extended to the [LaCe] and [LaLu] analogues. The results are consistent with a remarkable selectivity of the metal distribution within the molecule in the solid state, enhanced by the size difference between the different ions. This selectivity was reduced in solution, particularly for ions with the most similar radii. This unique entry into 4f-4f'' heterometallic chemistry establishes for the first time the difference between the selectivity in solution and that in the solid state, as a result of changes to the coordination that follow the dissociation of terminal ligands upon dissolution of the complexes.

Anions coordinating anions: analysis of the interaction between anionic Keplerate nanocapsules and their anionic ligands.

Keplerates are a family of anionic metal oxide spherical capsules containing up to 132 metal atoms and some hundreds of oxygen atoms. These capsules holding a high negative charge of -12 coordinate both mono-anionic and di-anionic ligands thus increasing their charge up to -42, even up to -72, which is compensated by the corresponding counter-cations in the X-ray structures. We present an analysis of the relative importance of several energy terms of the coordinate bond between the capsule and ligands like carbonate, sulphate, sulphite, phosphinate, selenate, and a variety of carboxylates, of which the overriding component is contributed by solvation/de-solvation effects.

Electronic and relativistic contributions to ion-pairing in polyoxometalate model systems.

Ion pairs and solubility related to ion-pairing in water influence many processes in nature and in synthesis including efficient drug delivery, contaminant transport in the environment, and self-assembly of materials in water. Ion pairs are difficult to observe spectroscopically because they generally do not persist unless extreme solution conditions are applied. Here we demonstrate two advanced techniques coupled with computational studies that quantify the persistence of ion pairs in simple solutions and offer explanations for observed solubility trends. The system of study, ([(CH3)4N]+,Cs)8[M6O19] (M = Nb,Ta), is a set of unique polyoxometalate salts whose water solubility increases with increasing ion-pairing, contrary to most ionic salts. The techniques employed to characterize Cs+ association with [M6O19]8- and related clusters in simple aqueous media are 133Cs NMR (nuclear magnetic resonance) quadrupolar relaxation rate and PDF (pair distribution function) from X-ray scattering. The NMR measurements consistently showed more extensive ion-pairing of Cs+ with the Ta-analogue than the Nb-analogue, although the electrostatics of the ions should be identical. Computational studies also ascertained more persistent Cs+-[Ta6O19] ion pairs than Cs+-[Nb6O19] ion pairs, and bond energy decomposition analyses determined relativistic effects to be the differentiating factor between the two. These distinctions are likely responsible for many of the unexplained differences between aqueous Nb and Ta chemistry, while they are so similar in the solid state. The X-ray scattering studies show atomic level detail of this ion association that has not been prior observed, enabling confidence in our structures for calculations of Cs-cluster association energies. Moreover, detailed NMR studies allow quantification of the number of Cs+ associated with a single [Nb6O19]8- or [Ta6O19]8- anion which agrees with the PDF analyses.