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Laplaza R, Wodrich MD, Corminboeuf C. Overcoming the Pitfalls of Computing Reaction Selectivity from Ensembles of Transition States. J Phys Chem Lett 2024; 15:7363-7370. [PMID: 38990895 DOI: 10.1021/acs.jpclett.4c01657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
The prediction of reaction selectivity is a challenging task for computational chemistry, not only because many molecules adopt multiple conformations but also due to the exponential relationship between effective activation energies and rate constants. To account for molecular flexibility, an increasing number of methods exist that generate conformational ensembles of transition state (TS) structures. Typically, these TS ensembles are Boltzmann weighted and used to compute selectivity assuming Curtin-Hammett conditions. This strategy, however, can lead to erroneous predictions if the appropriate filtering of the conformer ensembles is not conducted. Here, we demonstrate how any possible selectivity can be obtained by processing the same sets of TS ensembles for a model reaction. To address the burdensome filtering task in a consistent and automated way, we introduce marc, a tool for the modular analysis of representative conformers that aids in avoiding human errors while minimizing the number of reoptimization computations needed to obtain correct reaction selectivity.
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Affiliation(s)
- Ruben Laplaza
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Matthew D Wodrich
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Clemence Corminboeuf
- Laboratory for Computational Molecular Design, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- National Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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2
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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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3
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Hashemi A, Bougueroua S, Gaigeot MP, Pidko EA. ReNeGate: A Reaction Network Graph-Theoretical Tool for Automated Mechanistic Studies in Computational Homogeneous Catalysis. J Chem Theory Comput 2022; 18:7470-7482. [PMID: 36321652 DOI: 10.1021/acs.jctc.2c00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Exploration of the chemical reaction space of chemical transformations in multicomponent mixtures is one of the main challenges in contemporary computational chemistry. To remove expert bias from mechanistic studies and to discover new chemistries, an automated graph-theoretical methodology is proposed, which puts forward a network formalism of homogeneous catalysis reactions and utilizes a network analysis tool for mechanistic studies. The method can be used for analyzing trajectories with single and multiple catalytic species and can provide unique conformers of catalysts including multinuclear catalyst clusters along with other catalytic mixture components. The presented three-step approach has the integrated ability to handle multicomponent catalytic systems of arbitrary complexity (mixtures of reactants, catalyst precursors, ligands, additives, and solvents). It is not limited to predefined chemical rules, does not require prealignment of reaction mixture components consistent with a reaction coordinate, and is not agnostic to the chemical nature of transformations. Conformer exploration, reactive event identification, and reaction network analysis are the main steps taken for identifying the pathways in catalytic systems given the starting precatalytic reaction mixture as the input. Such a methodology allows us to efficiently explore catalytic systems in realistic conditions for either previously observed or completely unknown reactive events in the context of a network representing different intermediates. Our workflow for the catalytic reaction space exploration exclusively focuses on the identification of thermodynamically feasible conversion channels, representative of the (secondary) catalyst deactivation or inhibition paths, which are usually most difficult to anticipate based solely on expert chemical knowledge. Thus, the expert bias is sought to be removed at all steps, and the chemical intuition is limited to the choice of the thermodynamic constraint imposed by the applicable experimental conditions in terms of threshold energy values for allowed transformations. The capabilities of the proposed methodology have been tested by exploring the reactivity of Mn complexes relevant for catalytic hydrogenation chemistry to verify previously postulated activation mechanisms and unravel unexpected reaction channels relevant to rare deactivation events.
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Affiliation(s)
- Ali Hashemi
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Sana Bougueroua
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE) UMR8587, Universite Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Evry-Courcouronnes 91025, France
| | - Marie-Pierre Gaigeot
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE) UMR8587, Universite Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Evry-Courcouronnes 91025, France
| | - Evgeny A Pidko
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
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Menche M, Klein P, Hermsen M, Konrath R, Ghosh T, Wysocki J, Ernst M, Hashmi ASK, Schäfer A, Comba P, Schaub T. Ligand backbone influence on the enantioselectivity in the ruthenium‐catalyzed direct asymmetric reductive amination of ketones with NH3/H2 using binaphthyl‐substituted phosphines. ChemCatChem 2022. [DOI: 10.1002/cctc.202200543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maximilian Menche
- BASF SE Computational Chemistry Carl-Bosch-Str. 38 67056 Ludwigshafen GERMANY
| | - Philippe Klein
- Heidelberg University Catalysis Research Laboratory (CaRLa) Im Neuenheimer Feld 584 69120 Heidelberg GERMANY
| | - Marko Hermsen
- Heidelberg University CaRLa Im Neuenheimer Feld 584 69120 Heidelberg GERMANY
| | - Robert Konrath
- BASF SE Organic Synthesis Carl-Bosch-Str. 38 67056 Ludwigshafen GERMANY
| | - Tamal Ghosh
- Heidelberg University CaRLa Im Neuenheimer Feld 584 69120 Heidelberg GERMANY
| | - Jedrzej Wysocki
- Heidelberg University CaRLa Im Neuenheimer Flel 584 69120 Heidelberg GERMANY
| | - Martin Ernst
- BASF SE Organic Synthesis Carl-Bosch-Str. 38 67056 Ludwigshafen GERMANY
| | - A. Stephen K. Hashmi
- Heidelberg University Organic Chemistry Im Neuenheimer Feld 270 69120 Heidelberg GERMANY
| | - Ansgar Schäfer
- BASF SE Computational Chemistry Carl-Bosch-Str. 38 67056 Ludwigshafen GERMANY
| | - Peter Comba
- Heidelberg University Inorganic Chemistry Im Neuenheimer Feld 270 69120 Heidelberg GERMANY
| | - Thomas Schaub
- BASF SE Synthesis and Homogeneous Catalysis Carl-Bosch-Strasse 38 67056 Ludwigshafen GERMANY
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Krieger AM, Sinha V, Li G, Pidko EA. Solvent-Assisted Ketone Reduction by a Homogeneous Mn Catalyst. Organometallics 2022; 41:1829-1835. [PMID: 35910260 PMCID: PMC9326964 DOI: 10.1021/acs.organomet.2c00077] [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] [Indexed: 11/29/2022]
Abstract
![]()
The choice of a solvent
and the reaction conditions often defines
the overall behavior of a homogeneous catalytic system by affecting
the preferred reaction mechanism and thus the activity and selectivity
of the catalytic process. Here, we explore the role of solvation in
the mechanism of ketone reduction using a model representative of
a bifunctional Mn-diamine catalyst through density functional theory
calculations in a microsolvated environment by considering explicit
solvent and fully solvated ab initio molecular dynamics simulations
for the key elementary steps. Our computational analysis reveals the
possibility of a Meerwein–Ponndorf–Verley (MPV) type
mechanism in this system, which does not involve the participation
of the N–H moiety and the formation of a transition-metal hydride
species in ketone conversion. This path was not previously considered
for Mn-based metal–ligand cooperative transfer hydrogenation
homogeneous catalysis. The MPV mechanism is strongly facilitated by
the solvent molecules present in the reaction environment and can
potentially contribute to the catalytic performance of other related
catalyst systems. Calculations indicate that, despite proceeding effectively
in the second coordination sphere of the transition-metal center,
the MPV reaction path retains the enantioselectivity preference induced
by the presence of the small chiral N,N′-dimethyl-1,2-cyclohexanediamine ligand within the catalytic
Mn(I) complex.
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Affiliation(s)
- Annika M. Krieger
- Inorganic Systems Engineering Group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Vivek Sinha
- Inorganic Systems Engineering Group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Guanna Li
- Biobased Chemistry and Technology, Wageningen University, Bornse Weilanden 9, 6708WG Wageningen, The Netherlands
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Evgeny A. Pidko
- Inorganic Systems Engineering Group, Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Sinha V, Khramenkova E, Pidko EA. Solvent-mediated outer-sphere CO 2 electro-reduction mechanism over the Ag111 surface. Chem Sci 2022; 13:3803-3808. [PMID: 35432905 PMCID: PMC8966634 DOI: 10.1039/d1sc07119j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/23/2022] [Indexed: 12/01/2022] Open
Abstract
The electrocatalytic CO2 reduction reaction (CO2RR) is one of the key technologies of the clean energy economy. Molecular-level understanding of the CO2RR process is instrumental for the better design of electrodes operable at low overpotentials with high current density. The catalytic mechanism underlying the turnover and selectivity of the CO2RR is modulated by the nature of the electrocatalyst, as well as the electrolyte liquid, and its ionic components that form the electrical double layer (EDL). Herein we demonstrate the critical non-innocent role of the EDL for the activation and conversion of CO2 at a high cathodic bias for electrocatalytic conversion over a silver surface as a representative low-cost model cathode. By using a multiscale modeling approach we demonstrate that under such conditions a dense EDL is formed, which hinders the diffusion of CO2 towards the Ag111 electrocatalyst surface. By combining DFT calculations and ab initio molecular dynamics simulations we identify favorable pathways for CO2 reduction directly over the EDL without the need for adsorption to the catalyst surface. The dense EDL promotes homogeneous phase reduction of CO2via electron transfer from the surface to the electrolyte. Such an outer-sphere mechanism favors the formation of formate as the CO2RR product. The formate can undergo dehydration to CO via a transition state stabilized by solvated alkali cations in the EDL. In addition to the commonly accepted inner-sphere mechanism for e− transfer, we show that an outer-sphere electron transfer from the cathode to CO2 is operable at high overpotentials.![]()
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Affiliation(s)
- Vivek Sinha
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology Delft The Netherlands
| | - Elena Khramenkova
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology Delft The Netherlands
| | - Evgeny A Pidko
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology Delft The Netherlands
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