Open Access Article
Rubén
Laplaza‡
ab,
Jan-Grimo
Sobez‡
cd,
Matthew D.
Wodrich
ab,
Markus
Reiher
*cd and
Clémence
Corminboeuf
*ab
aLaboratory for Computational Molecular Design (LCMD), Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. E-mail: clemence.corminboeuf@epfl.ch
bNational Center for Competence in Research-Catalysis (NCCR-Catalysis), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
cLaboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland. E-mail: markus.reiher@phys.chem.ethz.ch
dNational Center for Competence in Research-Catalysis (NCCR-Catalysis), ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
First published on 18th May 2022
The computation of reaction selectivity represents an appealing complementary route to experimental studies and a powerful means to refine catalyst design strategies. Accurately establishing the selectivity of reactions facilitated by molecular catalysts, however, remains a challenging task for computational chemistry. The small free energy differences that lead to large variations in the enantiomeric ratio (er) represent particularly tricky quantities to predict with sufficient accuracy to be helpful for prioritizing experiments. Further complicating this problem is the fact that standard approaches typically consider only one or a handful of conformers identified through human intuition as pars pro toto of the conformational space. Obviously, this assumption can potentially lead to dramatic failures should key energetic low-lying structures be missed. Here, we introduce a multi-level computational pipeline leveraging the graph-based Molassembler library to construct an ensemble of molecular catalysts. The manipulation and interpretation of molecules as graphs provides a powerful and direct route to tailored functionalization and conformer generation that facilitates high-throughput mechanistic investigations of chemical reactions. The capabilities of this approach are validated by examining a Rh(III) catalyzed asymmetric C–H activation reaction and assessing the limitations associated with the underlying ligand design model. Specifically, the presence of remarkably flexible chiral Cp ligands, which induce the experimentally observed high level of selectivity, present a rich configurational landscape where multiple unexpected conformations contribute to the reported enantiomeric ratios (er). Using Molassembler, we show that considering about 20 transition state conformations per catalysts, which are generated with little human intervention and are not tied to “back-of-the-envelope” models, accurately reproduces experimental er values with limited computational expense.
Because the design of enantioselective catalysts often involves blocking access of a substrate to a reaction center from a non-desired orientation, large ligands are employed. Computationally, this represents a challenging situation, as these systems possess vast and complex conformational landscapes. Since er values vary dramatically based on very small free energy differences, it is critically important that any computational analysis systematically identifies the most stable of these structures, such that reliable er values can be obtained and the overarching catalyst design model validated or rejected. Generally, this “conformational problem” is treated using one of two diametrically opposed approaches, either by ignoring conformational flexibility altogether and applying chemical intuition to select the presumed “most reasonable” conformation pars pro toto or by comprehensive explorations of the conformational landscape using (ab initio) molecular dynamics coupled with enhanced sampling techniques (e.g., metadynamics with suitable collective variables).11 The latter fully accounts for the conformational flexibility of the catalyst but comes with a great computational cost, while the former can lead to completely erroneous results if human intuition fails to reliably identify the most important conformations.
While rotamer libraries12,13 and inexpensive potentials13–18 combined with sampling techniques (e.g., molecular dynamics or Monte Carlo simulations) facilitate the generation of conformational ensembles of ligands,19 substrates,13,20 or organocatalysts,15 the important functionalization process of catalyst design represents an additional computational hurdle. As such, numerous research groups have created computer programs that modifying catalyst structures through functionalization,21,22 including molSimplify23 and AARON,24,25 as well as evolutionary algorithms.26–30 Some of these also include additional functionalities that allow for basic conformational searching, but they continue to rely on sets of predefined conformers and are therefore subject to the same caveats previously mentioned. Because functionalization can open or close different regions of conformational space, using predefined conformations taken from parent catalysts may cause structurally distinct yet energetically meaningful conformers to be missed.
Given the conceptual and technical limitations discussed above, a clear need exists for an alternative approach that simultaneously merges comprehensive conformational searching with functionalization, such that chemical structures possessing enhanced flexibility can be easily manipulated without relying upon either molecular dynamic simulations or fixed rigid fragments. Such a tailored approach to automatically construct functionalized conformers would benefit from a graph-based treatment of chemical structure, which would allow even complex structural modifications to be undertaken easily. Here, we introduce a computational pipeline utilizing the graph-based (i.e., where molecular structures are interpreted as mathematical graphs where atoms are represented by nodes and bonds by edges) Molassembler library,31 a recently developed molecular construction and manipulation tool that couples automated functionalization with conformer generation on the fly to predict reaction enantioselectivity. We then demonstrate how the results of this pipeline can be used to further refine “back-of-the-envelope” catalyst design models.§
In the following sections, we describe our “design-and-sample” approach and its application to the asymmetric C–H functionalization of benzohydroxamates by chiral cyclopentadienyl Rh(III) catalysts.
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| Fig. 1 Schematic (left) and ball and stick (right) representation of the stereochemical model for catalyst 1C (R = Me, R′ = Ph), with the backwall and sidewall components highlighted. | ||
As a demonstration of the potential of our approach, we investigate the asymmetric C–H functionalization of benzohydroxamates to form dihydroisoquinolones catalyzed by chiral cyclopentadienyl (Cp) Rh(III) catalysts (Scheme 1a). Notably, the aforementioned high degree of rotational flexibility of the Cp moiety (as illustrated in red, Scheme 1b) along with the different size and flexibility of the hydroxamate substrate (blue, Scheme 1b) is known to strongly influence the experimentally observed enantiomeric ratio (er).33 Our results demonstrate the ability of our methodology to reproduce experimental er values by the automated location of mechanistic and conformational information that likely would be missed in a manual mechanism elucidation and design study relying on human input.
For a detailed description of the algorithms implemented in Molassembler we refer the reader to ref. 31.
assuming identical concentrations and pre-exponential factors throughout. Note that our choice of functional was motivated by previous literature reports,52 however, the use of alternative density functionals did not lead to significant degradation of the results (see ESI Fig. S4 and S5†).
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| Fig. 2 Flowchart of the proposed pipeline used to compute the effective relative free energies of the relevant pathways (ΔGTSeff). As a first step, the non-functionalized TS-template is interpreted as a graph by Molassembler, which tracks the spatial arrangement of all atoms and performs the required substitutions on the graph (i.e., adding the chiral Cp ligand). From the edited graph, a conformational ensemble respecting the first coordination shell of the Rh atom is generated. Execution of the first step takes less than a minute on average (see ESI† for timing details). As a second step, structures are optimized with the semiempirical GFN2-xTB approach, refined using DFT, and relative energies determined. See ESI† for exemplary code. | ||
:
4. Related chiral catalysts 2, 3 and 4 were also tested in combination with various protecting groups (i.e., R = OtBu, tBu, Me), as depicted in Scheme 1. Despite their obvious structural similarities, reaction selectivity varied significantly as a function of the chiral Cp ligand constituents. Specifically, three functional moieties were identified as key structural elements: two pro-chiral sidewalls (green, Fig. 1) and a back wall (blue, Fig. 1). Cramer et al.33 proposed a specific function for each of these structural units, where the sidewalls direct the hydroxamate substrate into a particular conformation while the backwall provides steric bulk that hinders the coordination of the incoming olefin on the back face of the hydroxamate. In this model, two possible relative orientations of the catalyst and the substrate were postulated to exist, with one, DR (where D denotes the Ph group points downward), leading to the (R)-product and the other, DS, to the (S)-product (Fig. 3). Here, the sidewall should disfavor the DS pathway, which leads to a more favorable DR conformation and a resulting high R
:
S enantiomeric ratio. Two additional pathways UR and US, which also lead to the (R)- and (S) products, presumably have a negligible contribution due to the assumed higher energy associated with a steric clash between the Ph group of styrene and the Cp ring (purple, Fig. 3) that occurs when coordinating the olefin with an upward pointing phenyl group; they were not considered in the original “back-of-the-envelope” model. Nonetheless, including these conformations in the analysis of reaction selectivity represents a prudent choice, particularly given that unforeseen low-energy conformations featuring the “up” configuration may play a key role in defining the er (Fig. 4).
As an initial demonstration of the Molassembler pipeline and its ability to reproduce accurately experimental results, we examined catalyst 1A (R = OtBu) in detail. Initially, a pool of transition state (TS) structures associated with the stereocontrolling olefin insertion step leading to C–C bond formation between the styrene and hydroxamate moiety for each of the four possible pathways (DR, DS, US and UR) was generated. Generation of this TS pool (which took only 46.8 seconds) only requires a representative template (in this case, an optimized TS with a bare Cp ligand) as an input. Following the generation, optimization, refinement, and removal of redundant conformers produced in the pipeline, a total of 15 TS conformations (6 DR, 4 DS, 2 UR, 3 US) were found for catalyst 1A (see Fig. 5a). Clearly evident from the superposition of these structures (Fig. 4) is that the rotational freedom of the Cp ring cannot be ignored if a holistic picture of the energetics and the resulting enantioselectivity is desired. Further analysis of the various TS structures also shows key contributions from the US and UR pathways. In fact, the lowest energy transition state (Fig. 4b, c and 5), which leads to formation of the (R)-product, actually originates from the UR pathway where the phenyl group of the styrene conceivably would “clash” with the Cp ring of the catalyst. This indicates a fundamental breakdown of the original model and illustrates the truly dynamic ability of the catalyst to adopt energetically favorable, yet non-intuitive conformations.
To determine the er of this catalyst, the computationally determined relative free energies (see Computational details for methods) of each of the conformations were Boltzmann weighted and the effective relative energy of each of the four pathways with respect to the separated catalyst and substrate determined (Fig. 5). Transition states were then separated as either pro-R or pro-S and the computationally derived er values computed.¶ As shown in Fig. 6a, the er estimations from our protocol (89
:
11, upper left square) closely parallels those determined by experiment (96
:
4) with catalyst 1A being very selective for the (R)-product.
In order to probe the ability of our workflow to reproduce experimental results as well as to predict the er values of unreported systems, we examined 11 other systems where the protecting group of the hydroxamate substrate (A = OtBu, B = tBu, C = Me) and the chiral Cp ligands (1–4, Scheme 1c) were changed. In this regard, the design of our computational protocol mirrors the experimental optimization efforts aimed at producing high R
:
S product ratios by invoking catalyst design techniques involving functionalization.
Comparing our computationally derived results with those obtained from experiment (colored boxes, Fig. 6), it is clear that the test case presented above is not a singular success, but rather that our computational workflow broadly reproduces experimental er values (darker green colors indicate closer matching with experimental values, Fig. 6a). This includes correct identification of species both that preferentially form the (R)- (e.g., 1A) and (S)-products (e.g., 3B). In addition to those species having experimental er values, we also computed the selectivity of five catalysts not tested in the laboratory. Notable amongst these is 3A, which is predicted to form the (R)-product, unlike 3B and 3C, which favor the (S)-product.
Given the importance of models in the development of ligand design, we reevaluated our results within the context of Cramer's “back-of-the-envelope” model by examining the er values of catalysts if only the lowest energy DR and DS conformers (Fig. 6b) or a Boltzmann weighting of all DR and DS conformers (Fig. 6c) are considered. In contrast to the er values obtained when all conformers (i.e., DR, DS, UR, US) are Boltzmann weighted (Fig. 6a), considering only conformers featuring downward pointing phenyl groups can lead to significant errors (red and orange colored boxes). Even in cases with seemingly good quantitative er agreement when only the DR and DS conformers are considered, the UR and US conformers were often found to be energetically lower-lying (indicated by asterisks, Fig. 6a). Thus, some of the predictions seen in Fig. 6b and c “accidently” arrive at the correct er because the (Boltzmann weighted) energy difference between the DR and DS conformers closely matches the difference between the UR and US conformers (i.e., the right answer for the wrong reason). Overall, these results demonstrate the utility of our pipeline not only as a screening tool for identifying selective catalysts prior to experimental testing, but also as a tool for developing better tailored design models.
Footnotes |
| † Electronic supplementary information (ESI) available. See https://doi.org/10.1039/d2sc01714h |
| ‡ These authors contributed equally to this work. |
| § In this work we examine rhodium-catalyzed asymmetric C–H functionalization, however the proposed pipeline is far more general. For selected examples involving other catalytic systems (including information on timing) the interested reader is encouraged to examine the ESI.† |
| ¶ In order to better track selectivities, we treated each pathway separately and constrained the relative orientation of styrene accordingly. This allowed us to easily track the pro-R or pro-S configurations, which was convenient but not necessary. As an alternative, all configurations could have been examined in parallel and classified a posteriori by examining the relative disposition of the olefin. |
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