Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

Altres ajuts: Acord transformatiu CRUE-CSICIn homogeneous catalysis solvent is an inherent part of the catalytic system. As such, it must be considered in the computational modeling. The most common approach to include solvent effects in quantum mechanical calculations is by means of continuum solvent models. When they are properly used, average solvent effects are efficiently captured, mainly those related with solvent polarity. However, neglecting atomistic description of solvent molecules has its limitations, and continuum solvent models all alone cannot be applied to whatever situation. In many cases, inclusion of explicit solvent molecules in the quantum mechanical description of the system is mandatory. The purpose of this article is to highlight through selected examples what are the reasons that urge to go beyond the continuum models to the employment of micro-solvated (cluster-continuum) of fully explicit solvent models, in this way setting the limits of continuum solvent models in computational homogeneous catalysis. These examples showcase that inclusion of solvent molecules in the calculation not only can improve the description of already known mechanisms but can yield new mechanistic views of a reaction. With the aim of systematizing the use of explicit solvent models, after discussing the success and limitations of continuum solvent models, issues related with solvent coordination and solvent dynamics, solvent effects in reactions involving small, charged species, as well as reactions in protic solvents and the role of solvent as reagent itself are successively considered

Origin of the Rate Acceleration in the C−C Reductive Elimination from Pt(IV)-complex in a [Ga4L6]12− Supramolecular Metallocage

Altres ajuts: Acord transformatiu CRUE-CSICThe reductive elimination on [(MeP)Pt(MeOH)(CH)], 2P, complex performed in MeOH solution and inside a [GaL] metallocage are computationally analysed by mean of QM and MD simulations and compared with the mechanism of gold parent systems previously reported [EtPAu(MeOH)(CH)], 2Au. The comparative analysis between the encapsulated Au(III) and Pt(IV)-counterparts shows that there are no additional solvent MeOH molecules inside the cavity of the metallocage for both systems. The Gibbs energy barriers for the 2P reductive elimination calculated at DFT level are in good agreement with the experimental values for both environments. The effect of microsolvation and encapsulation on the rate acceleration are evaluated and shows that the latter is far more relevant, conversely to 2Au. Energy decomposition analysis indicates that the encapsulation is the main responsible for most of the energy barrier reduction. Microsolvation and encapsulation effects are not equally contributing for both metal systems and consequently, the reasons of the rate acceleration are not the same for both metallic systems despite the similarity between them

Catalysis by [Ga4L6]12− metallocage on the Nazarov cyclization : the basicity of complexed alcohol is key

The Nazarov cyclization is investigated in solution and within K[GaL] supramolecular organometallic cage by means of computational methods. The reaction needs acidic condition in solution but works at neutral pH in the presence of the metallocage. The reaction steps for the process are analogous in both media: (a) protonation of the alcohol group, (b) water loss and (c) cyclization. The relative Gibbs energies of all the steps are affected by changing the environment from solvent to the metallocage. The first step in the mechanism, the alcohol protonation, turns out to be the most critical one for the acceleration of the reaction inside the metallocage. In order to calculate the relative stability of protonated alcohol inside the cavity, we propose a computational scheme for the calculation of basicity for species inside cavities and can be of general use. These results are in excellent agreement with the experiments, identifying key steps of catalysis and providing an in-depth understanding of the impact of the metallocage on all the reaction steps

Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [ML] 12- Supramolecular Organometallic Cage

Altres ajuts: Acord transformatiu CRUE-CSICThe encapsulation of molecular guests into supramolecular hosts is a complex molecular recognition process in which the guest displaces the solvent from the host cavity, while the host deforms to let the guest in. An atomistic description of the association would provide valuable insights on the physicochemical properties that guide it. This understanding may be used to design novel host assemblies with improved properties (i.e., affinities) toward a given class of guests. Molecular simulations may be conveniently used to model the association processes. It is thus of interest to establish efficient protocols to trace the encapsulation process and to predict the associated magnitudes Δ G and Δ G ⧧. Here, we report the calculation of the Gibbs energy barrier and Gibbs binding energy by means of explicit solvent molecular simulations for the [GaL] 12- metallocage encapsulating a series of cationic molecules. The Δ G ⧧ for encapsulation was estimated by means of umbrella sampling simulations. The steps involved were identified, including ion-pair formation and naphthalene rotation (from L ligands of the metallocage) during the guest's entrance. The Δ G values were computed using the attach-pull-release method. The results reveal the sensitivity of the estimates on the force field parameters, in particular on atomic charges, showing that higher accuracy is obtained when charges are derived from implicit solvent quantum chemical calculations. Correlation analysis identified some indicators for the binding affinity trends. All computed magnitudes are in very good agreement with experimental observations. This work provides, on one side, a benchmarked way to computationally model a highly charged metallocage encapsulation process. This includes a nonstandard parameterization and charge derivation procedure. On the other hand, it gives specific mechanistic information on the binding processes of [GaL] 12- at the molecular level where key motions are depicted. Taken together, the study provides an interesting option for the future design of metal-organic cages

A Reversible Phase Transition of 2D Coordination Layers by B–H∙∙∙Cu(II) Interactions in a Coordination Polymer

Materials that combine flexibility and open metal sites are crucial for myriad applications. In this article, we report a 2D coordination polymer (CP) assembled from CuII ions and a flexible meta-carborane-based linker [Cu2(L1)2(Solv)2]•xSolv (1-DMA, 1-DMF, and 1-MeOH; L1: 1,7-di(4-carboxyphenyl)-1,7-dicarba-closo-dodecaborane). 1-DMF undergoes an unusual example of reversible phase transition on solvent treatment (i.e., MeOH and CH2Cl2). Solvent exchange, followed by thermal activation provided a new porous phase that exhibits an estimated Brunauer-Emmett-Teller (BET) surface area of 301 m2 g−1 and is capable of a CO2 uptake of 41 cm3 g−1. The transformation is reversible and 1-DMF is reformed on addition of DMF to the porous phase. We provide evidence for the reversible process being the result of the formation/cleavage of weak but attractive B–H∙∙∙Cu interactions by a combination of single-crystal (SCXRD), powder (PXRD) X-ray diffraction, Raman spectroscopy, and DFT calculations.This research was funded by MEC grant CTQ2016-75150-R and the Generalitat de Catalunya (2017/SGR/1720) and the Spanish MINECO through the Severo Ochoa Centers of Excellence Program, under Grant SEV-2015-0496

Molecular Modeling of Encapsulation and Catalysis in Supramolecular Metallocages

En aquesta tesi, s'utilitzen simulacions de dinàmica molecular i càlculs de mecànica quàntica per investigar encapsulacions de molècules host (hostes) i augments molt significatius de la velocitat de reacció per a processos encapsulats en metalocaixes supramoleculars K12[Ga4L6], desenvolupades pel grup de Raymond. L'encapsulació de molècules host catiòniques s'ha investigat per establir un protocol per obtenir paràmetres del camp de forces validat respecte de dades experimentals. Les energies de Gibbs per al procés d'encapsulació es van calcular mitjançant simulacions MD utilitzant el mètode attach-pull-release (APR). En base a una bona concordança entre els càlculs i els experiments (amb una desviació absoluta d'aproximadament 2.0 kcal/mol), es proposa un procediment de parametrització per determinar els paràmetres no estàndard del sistema. La barrera d'energia de Gibbs per a l'encapsulació es va analitzar mitjançant l'anàlisi del potencial de força mitjana; aquest es construeix a partir de les simulacions umbrella sampling (US) amb el mètode d'anàlisi d'histograma ponderat (weighted histogram analysis method, WHAM). L'origen de les enormes acceleracions de la velocitat de reacció, comparables a les enzimàtiques, a les formacions d'enllaços C-C dels complexos d'AuIII i PtIV, i a la reacció de Nazarov, s'ha investigat mitjançant càlculs de QM guiats per simulacions de MD. Per als primers, l'anàlisi de l'acceleració de la velocitat es va fer en termes de microsolvatació i encapsulació. Els resultats mostren que el terme de microsolvatació és diferent per a aquests dos complexos metàl·lics (molt més gran per al complex AuIII que per al complex PtIV) i la interacció entre el complex metàl·lic i la metalocaixa és la principal contribució a la catàlisi a l'encapsulació. Per a la reacció de Nazarov, l'organització prèvia del substrat i l'estabilització del substrat protonat són fonamentals per a l'acceleració del procés. L'encapsulació del substrat per la metalocaixa indueix la preorganització. La protonació del substrat s'estabilitza substancialment dins de la metalocaixa, cosa que indica un canvi significatiu de la basicitat del substrat encapsulat, que és el factor principal en la catàlisi d' aquest procés. En general, els resultats presentats en aquesta tesi mostren la utilitat dels mètodes computacionals per aprofundir la comprensió dels processos d'encapsulació i catàlisi mitjançant metalocaixes supramoleculars.En esta tesis se emplean simulaciones de dinámica molecular y cálculos de mecánica cuántica para investigar tanto encapsulaciones de moléculas host (huéspedes), como aumentos muy significativos de la velocidad de reacción para procesos encapsulados en metalocajas supramoleculares K12[Ga4L6]. Esta metalocajas han sido desarrolladas por el grupo de Raymond. La encapsulación de moléculas host catiónicas se ha investigado para establecer un protocolo para obtener parámetros del campo de fuerzas validado respecto a datos experimentales. Las energías de Gibbs para el proceso de encapsulación se calcularon mediante simulaciones MD utilizando el método attach-pull-release (APR). Sobre la base de una buena concordancia entre los cálculos y los experimentos (con una desviación absoluta de aproximadamente 2.0 kcal/mol), se propone un procedimiento de parametrización para determinar los parámetros no estándar del sistema. La barrera de energía de Gibbs para la encapsulación se analizó mediante el análisis del potencial de la fuerza media; este se construye a partir de las simulaciones umbrella sampling (US) con el método de análisis de histograma ponderado (weighted histogram analysis method, WHAM). El origen de las enormes aceleraciones de la velocidad de reacción, comparables a las enzimáticas, en las formaciones de enlaces C-C de los complejos de AuIII y PtIV, y en la reacción de Nazarov se ha investigado mediante cálculos de QM guiados por simulaciones de MD. Para el primero, el análisis de la aceleración de la velocidad se realizó en términos de microsolvatación y encapsulación. Los resultados muestran que el término de microsolvatación es diferente para estos dos complejos metálicos (mucho mayor para el complejo AuIII que para el complejo PtIV) y la interacción entre el complejo metálico y la metalocaja es la principal contribución a la catálisis en la encapsulación. Para la reacción de Nazarov, la organización previa del sustrato y la estabilización del sustrato protonado son fundamentales para esta aceleracion del proceso. La encapsulación del sustrato por el metalocaja induce a su preorganización. La protonación del sustrato se estabiliza sustancialmente dentro de la metalocaja, lo que indica un cambio significativo de la basicidad del sustrato encapsulado, que es el factor principal en esta catálisis en este proceso. En general, los resultados presentados en esta tesis muestran la utilidad de los métodos computacionales para profundizar la comprensión de los procesos de encapsulación y catálisis mediante metalocajas supramoleculares.In this thesis, molecular dynamics simulations and quantum chemical calculations are employed to investigate guest-encapsulations and rate-enhancements in a K12[Ga4L6] supramolecular metallocage developed by the Raymond group. Encapsulation of cationic guest molecules has been investigated to establish a protocol validated against numerical experimental data. Their binding Gibbs energies were computed with MD simulations using the attach-pull-release (APR) approach. Based on the excellent agreement between calculations and experiments (the absolute deviation of up to ca. 2.0 kcal/mol), a parametrization procedure is proposed to better quantify the non-standard parameters of the system. The Gibbs energy barrier for encapsulation is also determined by the potential of mean force constructed from the umbrella sampling (US) simulations with the weighted histogram analysis method (WHAM). A description at a molecular level of the encapsulation is obtained. The origin of enzymelike rate enhancements in C-C bond formations from Au(III) and Pt(IV) complexes and in the Nazarov reaction have been investigated by QM calculations guided by MD simulations. For the former, the analysis of the rate acceleration performed in terms of microsolvation and encapsulation shows that microsolvation term is different for these two metal complexes (much larger for Au(III) complex than for Pt(IV) complex) and the interaction between the metal complex and metallocage is the main contribution to the catalysis upon the encapsulation. For the Nazarov reaction, the pre-organization of the substrate and the stabilization of the protonated substrate are fundamental to this rate enhancement. The encapsulation of the substrate by the metallocage induces the substrate pre-organization. The protonation of the substrate is substantially stabilized by the metallocage, indicating a shift of the basicity of the alcohol substrate in the metallocage which is the main factor in this catalysis. Overall, the results presented in this thesis show the usefulness of computational methods to deepen understanding encapsulation and catalytic processes in supramolecular metallocage

Reaction rate inside the cavity of [Ga4L6]12− supramolecular metallocage is regulated by the encapsulated solvent

In the present study the dependence of the reaction rate of carbon-carbon reductive elimination from R3PAu(MeOH)(CH3)2 (R=Me, Et) complexes inside [Ga4L6]12− metallocage on the nature of the phosphine ligand is investigated by computational means. The reductive elimination mechanism is analyzed in methanol solution and inside the metallocage. Classical molecular dynamics simulations reveal that the smaller the gold complex (which depends on the phosphine ligand size) the larger the number of solvent molecules encapsulated. The size of the phosphine ligands defines the space that is left available inside the cavity that can be occupied by solvent molecules. The Gibbs energy barriers calculated at DFT level, in excellent agreement with experiment both in solution and in the metallocage, show that the presence/absence of explicit solvent molecules inside the cavity significantly modifies the reaction rate

Microsolvation and Encapsulation Effects on Supramolecular Catalysis : CC Reductive Elimination inside [Ga4L6] 12- Metallocage

The host effect of the supramolecular [Ga4L6]12- tetrahedral metallocage on reductive elimination of substrate by encapsulated Au(III) complexes is investigated by means of computational methods. The behavior of the reactants in solution and within the metallocage is initially evaluated by means of classical molecular dynamics simulations. These results guided the selection of proper computational models to describe the reaction in solution and inside the metallocage at the DFT level. The calculated Gibbs energy barriers are in very good agreement with experiment both in solution and inside the metallocage. The analysis in solution revealed that microsolvation around the Au(III) complex increases the Gibbs energy barrier. The analysis within the metallocage shows that its encapsulation favors the reaction. The process can be formally described as removing explicit microsolvation around the gold complex and encapsulating the metal complex inside the metallocage. Both processes are important for the reaction, but the removal of the solvent molecules surrounding the Au(III) metal complex is fundamental for the reduction of the reaction barrier. The energy decomposition analysis of the barrier among strain, interaction, and thermal terms shows that strain term is very low whereas the contribution of thermal (entropic) effects is moderate. Interestingly, the key term responsible for reducing the Gibbs energy barrier is the interaction. This term can be mainly associated with electrostatic interactions in agreement with previous examples in the literature

A reversible phase transition of 2D coordination layers by B-H···Cu(II) interactions in a coordination polymer

Materials that combine flexibility and open metal sites are crucial for myriad applications. In this article, we report a 2D coordination polymer (CP) assembled from CuII ions and a flexible meta-carborane-based linker [Cu(L1)(Solv)]•xSolv (1-DMA, 1-DMF, and 1-MeOH; L1: 1,7-di(4-carboxyphenyl)-1,7-dicarba-closo-dodecaborane). 1-DMF undergoes an unusual example of reversible phase transition on solvent treatment (i.e., MeOH and CHCl). Solvent exchange, followed by thermal activation provided a new porous phase that exhibits an estimated Brunauer-Emmett-Teller (BET) surface area of 301 m g and is capable of a CO uptake of 41 cm g. The transformation is reversible and 1-DMF is reformed on addition of DMF to the porous phase. We provide evidence for the reversible process being the result of the formation/cleavage of weak but attractive B-H···Cu interactions by a combination of single-crystal (SCXRD), powder (PXRD) X-ray diffraction, Raman spectroscopy, and DFT calculations