A recent advance in the synthesis of alkenylated arenes was the demonstration that the Pd(OAc)2 catalyst precursor gives >95% selectivity toward styrene from ethylene and benzene under optimized conditions using excess Cu(II) carboxylate as the in situ oxidant [ Organometallics 2019, 38(19), 3532−3541]. To understand the mechanism underlying this catalysis, we applied density functional theory (DFT) calculations in combination with experimental studies. From DFT calculations, we determined the lowest-energy multimetallic Pd and Pd–Cu mixed metal species as possible catalyst precursors. From the various structures, we determined the cyclic heterotrinuclear complex PdCu2(μ-OAc)6 to be the global minimum in Gibbs free energy under conditions of excess Cu(II). For cyclic PdCu2(μ-OAc)6 and the parent [Pd(μ-OAc)2]3, we evaluated the barriers for benzene C–H activation through concerted metalation deprotonation (CMD). The PdCu2(μ-OAc)6 cyclic trimer leads to a CMD barrier of 33.5 kcal/mol, while the [Pd(μ-OAc)2]3 species leads to a larger CMD barrier at >35 kcal/mol. This decrease in the CMD barrier arises from the insertion of Cu(II) into the trimetallic species. Because cyclic PdCu2(μ-OAc)6 is likely the predominant species under experimental conditions (the Cu to Pd ratio is 480:1 at the start of catalysis) with a predicted CMD barrier within the range of the experimentally determined activation barrier, we propose that cyclic PdCu2(μ-OAc)6 is the Pd species responsible for catalysis and report a full reaction mechanism based on DFT calculations. For catalytic conversion of benzene and ethylene to styrene at 120 °C using Pd(OAc)2 as the catalyst precursor and Cu(OPiv)2 (OPiv = pivalate) as the oxidant, an induction period of ∼1 h was observed, followed by catalysis with a turnover frequency of ∼2.3 × 10–3 s–1. In situ1H NMR spectroscopy experiments indicate that during the induction period, Pd(OAc)2 is likely converted to cyclic PdCu2(η2-C2H4)3(μ-OPiv)6, which is consistent with the calculations and consistent with the proposal that the active catalyst is the ethylene-coordinated heterotrinuclear complex cyclic PdCu2(η2-C2H4)3(μ-OPiv)6.
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Ensemble Effects on Allylic Oxidation within Explicit Solvation Environments
Umbrella-sampling density functional theory molecular dynamics (DFT-MD) has been employed to
study the full catalytic cycle of the allylic oxidation of cyclohexene using a Cu(II) 7-amino-6-((2-
hydroxybenzylidene)amino)quinoxalin-2-ol complex in acetonitrile to create cyclohexenone and H2O
as products. After the initial H-atom abstraction step, two different reaction pathways have been
identified that are distinguished by the participation of alkyl hydroperoxide (referred to as the “open”
cycle) versus the methanol side-product (referred to as the “closed” cycle) within the catalyst recovery
process. Importantly, both pathways involve dehydrogenation and re-hydrogenation of the -NH2
group bound to the Cu-site - a feature that is revealed from the ensemble sampling of configurations
of the reactive species that are stabilized within the explicit solvent environment of the simulation.
Estimation of the energy span from the experimental turnover frequency yields an approximate value
of 22.7 kcal/mol at 350 K. Whereas the closed cycle value is predicted to be 26.2 kcal/mol, the open
cycle value at 16.5 kcal/mol. Both pathways are further consistent with the equilibrium between
Cu(II) and Cu(III) than what has previously been observed. In comparison to prior static DFT
calculations, the ensemble of of both solute and solvent configurations has helped to reveal a breadth
of processes that underpin the full catalytic cycle yielding a more comprehensive understanding of
the importance of radical reactions and catalysis recovery.
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- Award ID(s):
- 1934725
- NSF-PAR ID:
- 10244157
- Date Published:
- Journal Name:
- Dalton transactions
- ISSN:
- 1477-9226
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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ABSTRACT In this work, by means of quantum chemistry (Density Functional Theory (DFT), PW6B95/def2-TZVPP; DLPNO-CCSD(T)/CBS), HCN polymerization [(HCN)1 − 4] initiated and catalysed by a siloxyl radical (Si-O•) on a model silica surface is analysed. Linear HCN polymers (pHCN) are obtained by a radical initiated mechanism at a SiO• site and are characterized by a -(HC-N)- skeleton due to radical localization on the terminal N atom and radical attack on the C centre. NC heterocycles are formed by cyclization of the linear SiO-(HCN)3 − 4 and are always thermodynamically preferred over their linear counterparts, acting as thermodynamic sinks. Of particular interest to the astrochemistry community is the formation of the N-heterocycle 1,3,5-triazine that can be released into the gas phase at relatively low T (ΔG† = 23.3 kcal/mol). Full hydrogenation of SiO-(HCN•) follows two reaction channels with products: (a) SiO-CH3 + •NH2 or (b) amino-methanol + Si•, though characterized by slow kinetics. Nucleophilic addition of H2O to the electron-rich SiO-(HCN•) shows an unfavourable thermodynamics as well as a high-activation energy. The cleavage of the linear (HCN)1−4 from the SiO• site also shows a high thermodynamic energy penalty (ΔG≥82.0 kcal/mol). As a consequence, the silicate surface will be passivated by a chemically active ‘pHCN brush’ modifying the surface physico-chemical properties. The prospect of surface-catalysed HCN polymers exhibiting a high degree of chemical reactivity and proposed avenues for the formation of 1,3,5-triazine and amino-methanol opens exciting new chemical pathways to Complex Organic Matter formation in astrochemistry.
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Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the cis state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in cis , a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the cis conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the cis and trans states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline cis and trans states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in cis , leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in trans . The ensemble containing cis prolines also matches more closely to in vitro circular dichroism data than the all- trans ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with in vitro data.more » « less
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The catalytic effects of iridium pincer complexes for the hydrogenation of carbon dioxide were investigated with the Unified Reaction Valley Approach (URVA), exploring the reaction mechanism along the reaction path traced out by the reacting species on the potential energy surface. Further details were obtained with the Local Mode Analysis performed at all stationary points, complemented by the Natural Bond Orbital and Bader’s Quantum Atoms in Molecules analyses. Each of the five reaction paths forming the catalytic cycle were calculated at the DFT level complemented with DLPNO-CCSD(T) single point calculations at the stationary points. For comparison, the non-catalytic reaction was also investigated. URVA curvature profiles identified all important chemical events taking place in the non-catalyzed reaction and in the five reactions forming the catalytic cycle, and their contribution to the activation energy was disclosed. The non-catalytic reaction has a large unfavorable activation energy of 76.3 kcal/mol, predominately caused by HH bond cleave in the H2 reactant. As shown by our study, the main function of the iridium pincer catalyst is to split up the one–step non-catalytic reaction into an energy efficient multistep cycle, where HH bond cleavage is replaced by the cleavage of a weaker IrH bond with a small contribution to the activation energy. The dissociation of the final product from the catalyst requires the cleavage of an IrO bond, which is also weak, and contributes only to a minor extent to the activation energy. This, in summary, leads to the substantial lowering of the overall activation barrier by about 50 kcal/mol for the catalyzed reaction. We hope that this study inspires the community to add URVA to their repertoire for the investigation of catalysis reactions.more » « less
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Abstract Copper‐exchanged zeolites are useful for stepwise conversion of methane to methanol at moderate temperatures. This process also generates some over‐oxidation products like CO and CO2. However, mechanistic pathways for methane over‐oxidation by copper‐oxo active sites in these zeolites have not been previously described. Adequate understanding of methane over‐oxidation is useful for developing systems with higher methanol yields and selectivities. Here, we use density functional theory (DFT) to examine methane over‐oxidation by [Cu3O3]2+active sites in zeolite mordenite MOR. The methyl group formed after activation of a methane C−H bond can be stabilized at a μ‐oxo atom of the active site. This μ‐(O−CH3) intermediate can undergo sequential hydrogen atom abstractions till eventual formation of a copper‐monocarbonyl species. Adsorbed formaldehyde, water and formates are also formed during this process. The overall mechanistic path is exothermic, and all intermediate steps are facile at 200 °C. Release of CO from the copper‐monocarbonyl costs only 3.4 kcal/mol. Thus, for high methanol selectivities, the methyl group from the first hydrogen atom abstraction step
must be stabilizedaway from copper‐oxo active sites. Indeed, it must be quickly trapped at an unreactive site (short diffusion lengths) while avoiding copper‐oxo species (large paths between active sites). This stabilization of the methyl group away from the active sites is central to the high methanol selectivities obtained with stepwise methane‐to‐methanol conversion.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D1DT00785H
