An explicit account of solvation is essential for modeling Suzuki–Miyaura coupling in protic solvents

Zeifman, Alexey A.; Novikov, Fedor N.; Stroylov, Viktor S.; Stroganov, Oleg V.; Svitanko, Igor V.; Chilov, Ghermes G.

doi:10.1039/c5dt03126e

Cited by 7 publications

(6 citation statements)

References 41 publications

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“…The Gibbs energy profile for the reductive elimination step of Suzuki-Miyaura couplings have been computed using explicit and implicit solvation approaches in a diverse set of solvents (benzene, toluene, DMF, ethanol and water) [30]. Although a good agreement between both approaches was obtained for aprotic solvents, the correlation was poor for protic solvents.…”

Section: Success and Limitations Of Continuum Solvent Modelsmentioning

confidence: 99%

Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

2021

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In 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.

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Section: Success and Limitations Of Continuum Solvent Modelsmentioning

confidence: 99%

Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

2021

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“…Whereas a reasonable correlation between both solvent representations was found in aprotic solvents, the correlation was poor for ethanol and water. The paper stresses the need for considering explicit solvation for modeling Pd-catalyzed reactions in protic solvents [104]. Indeed, this can be a rather general conclusion.…”

Section: The Solvent: Chemical and Theoretical Modelmentioning

confidence: 75%

“…A similar approach was employed to compare explicit and implicit solvation models in modeling the free energy profile of the reductive elimination step in Suzuki-Miyaura coupling. The reductive elimination of two Ph ligands from Pd(PPh3)2 was modelled in a diverse set of solvents (benzene, toluene, DMF, ethanol and water) using both QM/MM molecular dynamics simulations and a continuum model (SMD) [104]. Whereas a reasonable correlation between both solvent representations was found in aprotic solvents, the correlation was poor for ethanol and water.…”

Section: The Solvent: Chemical and Theoretical Modelmentioning

confidence: 99%

What Makes a Good (Computed) Energy Profile?

Eisenstein

Ujaque

Lledós

2020

New Directions in the Modeling of Organometallic Reactions

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Coupled-Cluster method with single and double excitations and perturbative triples DFT Density Functional Theory DLPNO Domain based local pair natural orbital coupled cluster method with single-, double-and perturbative triple excitations ESI-MS Electrospray ionization mass spectrometry HF Hartree-Fock IGRRHO Ideal gas/rigid rotor/harmonic oscillator MD Molecular Dynamics PES Potential Energy Surface

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“… Incorporating explicit solvent molecules produced more reliable computed activation free energy barriers in modelling of numerous reaction mechanisms [ 29 , 30 ]. Discrete solvent molecules can capture solvent dynamics [ 31 ] and may play a significant role in chemical reactions that implicit solvation models fail to capture [ 32 , 33 ]. …”

Section: Introductionmentioning

confidence: 99%

“…Discrete solvent molecules can capture solvent dynamics [ 31 ] and may play a significant role in chemical reactions that implicit solvation models fail to capture [ 32 , 33 ].…”

Section: Introductionmentioning

confidence: 99%

A Molecular-Wide and Electron Density-Based Approach in Exploring Chemical Reactivity and Explicit Dimethyl Sulfoxide (DMSO) Solvent Molecule Effects in the Proline Catalyzed Aldol Reaction

Cukrowski¹,

Dhimba²,

Riley³

2022

Molecules

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Modelling of the proline (1) catalyzed aldol reaction (with acetone 2) in the presence of an explicit molecule of dimethyl sulfoxide (DMSO) (3) has showed that 3 is a major player in the aldol reaction as it plays a double role. Through strong interactions with 1 and acetone 2, it leads to a significant increase of energy barriers at transition states (TS) for the lowest energy conformer 1a of proline. Just the opposite holds for the higher energy conformer 1b. Both the ‘inhibitor’ and ‘catalyst’ mode of activity of DMSO eliminates 1a as a catalyst at the very beginning of the process and promotes the chemical reactivity, hence catalytic ability of 1b. Modelling using a Molecular-Wide and Electron Density-based concept of Chemical Bonding (MOWED-CB) and the Reaction Energy Profile–Fragment Attributed Molecular System Energy Change (REP-FAMSEC) protocol has shown that, due to strong intermolecular interactions, the HN-C-COOH (of 1), CO (of 2), and SO (of 3) fragments drive a chemical change throughout the catalytic reaction. We strongly advocate exploring the pre-organization of molecules from initially formed complexes, through local minima to the best structures suited for a catalytic process. In this regard, a unique combination of MOWED-CB with REP-FAMSEC provides an invaluable insight on the potential success of a catalytic process, or reaction mechanism in general. The protocol reported herein is suitable for explaining classical reaction energy profiles computed for many synthetic processes.

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An explicit account of solvation is essential for modeling Suzuki–Miyaura coupling in protic solvents

Cited by 7 publications

References 41 publications

Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

What Makes a Good (Computed) Energy Profile?

A Molecular-Wide and Electron Density-Based Approach in Exploring Chemical Reactivity and Explicit Dimethyl Sulfoxide (DMSO) Solvent Molecule Effects in the Proline Catalyzed Aldol Reaction

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