Scope and Challenge of Computational Methods for Studying Mechanism and Reactivity in Homogeneous Catalysis

Interplay between diphenyl diselenide and copper: Impact on D. melanogaster survival, behavior, and biochemical parameters

Copper (Cu2+) is a biologically essential element that participates in numerous physiological processes. However, elevated concentrations of copper have been associated with cellular oxidative stress and neurodegenerative diseases. Organo‑selenium compounds such as diphenyl diselenide (DPDS) have in vitro and in vivo antioxidant properties. Hence, we hypothesized that DPDS may modulate the toxicity of Cu2+ in Drosophila melanogaster. The acute effects (4 days of exposure) caused by a high concentration of Cu2+ (3 mM) were studied using endpoints of toxicity such as survival and behavior in D. melanogaster. The potential protective effect of low concentration of DPDS (20 μM) against Cu2+ was also investigated. Adult flies aged 1-5 days post-eclosion (both sexes) were divided into four groups: Control, DPDS (20 μM), CuSO4 (3 mM), and the combined exposure of DPDS (20 μM) and CuSO4 (3 mM). Survival, biochemical, and behavioral parameters were determined. Co-exposure of DPDS and CuSO4 increased acetylcholinesterase (AChE) activity and the generation of reactive oxygen species (ROS as determined by DFCH oxidation). Contrary to our expectation, the co-exposure reduced survival, body weight, locomotion, catalase activity, and cell viability in relation to control group. Taken together, DPDS potentiated the Cu2+ toxicity.

Predicting the propene stereoselectivity on transition metal catalysts: A daunting task for density functional theory

Thanks to recent developments in hardware and software, quantum chemical methods are increasingly used for interpreting the complex mechanisms underlying polymerization reaction by homogeneous catalysis. Unfortunately, the dimensions of even the smallest realistic models are too large to permit the use of state-of-the-art composite wave function methods. Under these circumstances, density functional theory still offers the best compromise between cost and accuracy. However, comprehensive benchmarks of different functionals are not yet available for this important research field. The main aim of the present paper is to fill this gap by performing an unbiased comparison of several density functionals and continuum solvent models for the stereo-control in the propylene polymerization on prototypical catalysts inducing different reaction mechanisms. While it was not possible to define a unique computational protocol providing the best results in all the situations, the B3PW91 functional in conjunction with D3 empirical dispersions and the solvent model density solvent model performs remarkably well for three out of the four investigated catalysts. Under such circumstances, it is recommended to compare the results delivered by different models when approaching additional classes of catalysts.

Exploring the mechanism of the reductive amination of acetophenones via the Borch approach: the role of the acid catalyst

The energetic viability of several mechanistic variations of the reductive amination of acetophenones via the Borch approach was re-examined through density functional theory calculations. The crucial involvement of the acid catalyst is evident not only in the elimination of water, but also in the initial nucleophilic step. This role increases with the electron-donating capability of the substituent positioned at the para-position of acetophenone.

A human-machine interface for automatic exploration of chemical reaction networks

Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible intermediates is computationally too demanding. This renders brute-force explorations unfeasible, while explorations with completely pre-defined intermediates or hard-wired chemical constraints, such as element-specific coordination numbers, are not flexible enough for complex chemical systems. Here, we introduce a STEERING WHEEL to guide an otherwise unbiased automated exploration. The STEERING WHEEL algorithm is intuitive, generally applicable, and enables one to focus on specific regions of an emerging network. It also allows for guiding automated data generation in the context of mechanism exploration, catalyst design, and other chemical optimization challenges. The algorithm is demonstrated for reaction mechanism elucidation of transition metal catalysts. We highlight how to explore catalytic cycles in a systematic and reproducible way. The exploration objectives are fully adjustable, allowing one to harness the STEERING WHEEL for both structure-specific (accurate) calculations as well as for broad high-throughput screening of possible reaction intermediates.

Stereocontrol via Propeller Chirality in FLP-Catalyzed Asymmetric Hydrogenation

Utilization of chiral frustrated Lewis pairs as catalysts in enantioselective hydrogenation of unsaturated molecules represents a promising approach in asymmetric synthesis. In our effort to improve our current understanding of the factors governing the stereoselectivity in these catalytic processes, herein we examined the mechanism of direct hydrogenation of aromatic enamines catalyzed by a binaphthyl-based chiral amino-borane. Our computational analysis reveals that only one particular conformer of the key borohydride reaction intermediate can be regarded as a reactive form of this species. This borohydride conformer has a well-defined chiral propeller shape, which induces facial selectivity in the hydride transfer to pro-chiral iminium intermediates. The propeller chirality of the reactive borohydride conformer is generated by the axially chiral binaphthyl scaffold of the amino-borane catalyst through stabilizing π-π stacking interactions. This new computational insight can be readily used to interpret the high degree of stereoinduction observed for these reactions. We expect that the concept of chirality relay could be further exploited in catalyst design endeavors.

Scaffold-Oriented Asymmetric Catalysis: Conformational Modulation of Transition State Multivalency during a Catalyst-Controlled Assembly of a Pharmaceutically Relevant Atropisomer

A new class of superbasic, bifunctional peptidyl guanidine catalysts is presented, which enables the organocatalytic, atroposelective synthesis of axially chiral quinazolinediones. Computational modeling unveiled the conformational modulation of the catalyst by a novel phenyl urea N-cap, that preorganizes the structure into the active, folded state. A previously unanticipated noncovalent interaction involving a difluoroacetamide acting as a hybrid mono- or bidentate hydrogen bond donor emerged as a decisive control element inducing atroposelectivity. These discoveries spurred from a scaffold-oriented project inspired from a fascinating investigational BTK inhibitor featuring two stable chiral axes and relies on a mechanistic framework that was foreign to the extant lexicon of asymmetric catalysis.

DFT-Guided Mechanistic Insights into Chemodivergence: A Mixed Explicit-Implicit Solvent Description to Dictate the Chemoselectivity

Herein we report a density functional theory (DFT)-guided mechanistic investigation of the nitrile reduction reaction, which exhibits a solvent-dependent chemodivergence. This study reveals an interesting mechanistic picture, highlighting the exact role of a protic solvent, isopropanol, in regulating the reaction outcome. The explicit solvent effect involving polar protic isopropanol favors imine metathesis by proton hopping through stepwise addition and elimination steps and thus produces a secondary amine as the final product. In contrast, the nonpolar solvent n-hexane is incapable of facilitating the proton migration and stops the solvent-assisted imine metathesis. As a result, only primary amines are obtained as the final product. This DFT study provides a recipe for the choice of solvents that can dictate chemoselectivity in product formation.

Tuning the Catalytic Activity of a Pincer Complex of Rhodium(I) by Supramolecular and Redox Stimuli

We report the rhodium(I) complex [Rh(CNC-NDI)(CO)]+ , in which CNC-NDI refers to a pincer-CNC ligand decorated with a naphthalenediimide moiety. Due to the presence of the planar CNC ligand and the naphthalenediimide moiety, the electronic nature of the complex can be modulated by means of supramolecular and redox stimuli, respectively. The metal complex shows a strong π-π-stacking interaction with coronene. This interaction has an impact on the electron-richness of the metal, as demonstrated by the shifting of the ν(CO) stretching band to a lower frequency. The addition of tetrabutylammonium fluoride facilitates the sequential one- and two-electron reduction of the NDI moiety of the ligand, thus resulting in a situation in which the ligand can increase its electron-donor strength in two levels. The nature of the interaction with the fluoride anion was studied computationally. The catalytic activity of the [Rh(CNC-NDI)(CO)]+ complex was tested in the cycloisomerization of alkynoic acids, where it is observed that the activity of the catalyst can be modulated between four levels of activity, which correspond to i) the use of the unmodified catalyst, ii) catalyst+coronene, iii) catalyst+2 equivalents of fluoride, and iv) catalyst+5 equivalents of fluoride.

PyConSolv: A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent

We introduce PyConSolv, a freely available Python package that automates the generation of conformers of metal- and nonmetal-containing complexes in explicit solvent, through classical molecular dynamics simulations. Using a streamlined workflow and interfacing with widely used computational chemistry software, PyConSolv is an all-in-one tool for the generation of conformers in any solvent. Input requirements are minimal; only the geometry of the structure and the desired solvent in xyz (XMOL) format are needed. The package can also account for charged systems, by including arbitrary counterions in the simulation. A bonded model parametrization is performed automatically, utilizing AmberTools, ORCA, and Multiwfn software packages. PyConSolv provides a selection of preparametrized solvents and counterions for use in classical molecular dynamics simulations. We show the applicability of our package on a number of (transition-metal-containing) systems. The software is provided open source and free of charge.

Multi-Time-Scale Simulation of Complex Reactive Mixtures: How Do Polyoxometalates Form?

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.

Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes

The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.

Electron-rich benzofulvenes as effective dipolarophiles in copper(i)-catalyzed asymmetric 1,3-dipolar cycloaddition of azomethine ylides

A series of benzofulvenes without any electron-withdrawing substituents were employed as 2π-type dipolarophiles for the first time to participate in Cu(i)-catalyzed asymmetric 1,3-dipolar cycloaddition (1,3-DC) reactions of azomethine ylides. An intrinsic non-benzenoid aromatic characteristic from benzofulvenes serves as a key driving force for activation of the electron-rich benzofulvenes. Utilizing the current methodology, a wide range of multi-substituted chiral spiro-pyrrolidine derivatives containing two contiguous all-carbon quaternary centers were formed in good yield with exclusive chemo-/regioselectivity and high to excellent stereoselectivity. Computational mechanistic studies elucidate the origin of the stereochemical outcome and the chemoselectivity, in which the thermostability of these cycloaddition products is the major factor.

The entropic penalty for associative reactions and their physical treatment during routine computations

A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 Δ_rG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol^-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol^-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol^-1 (classic) and underestimated by 2 kcal mol^-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol^-1 lower than barriers obtained with WFT.

Regeneration and Degradation in a Biomimetic Polyoxometalate Water Oxidation Catalyst

Complete understanding of catalytic cycles is required to advance the design of water oxidation catalysts, but it is difficult to attain, due to the complex factors governing their reactivity and stability. In this study, we investigate the regeneration and degradation pathways of the highly active biomimetic water oxidation catalyst [Mn³⁺ ₂Mn⁴⁺ ₂V₄O₁₇(OAc)₃]^3-, thereby completing its catalytic cycle. Beginning with the deactivated species [Mn³⁺ ₄V₄O₁₇(OAc)₂]^4- left over after O₂ evolution, we scrutinize a network of reaction intermediates belonging to two alternative water oxidation cycles. We find that catalyst regeneration to the activated species [Mn⁴⁺ ₄V₄O₁₇(OAc)₂(OH)(H₂O)]^- proceeds via oxidation of each Mn center, with one water ligand being bound during the first oxidation step and a second water ligand being bound and deprotonated during the final oxidation step. ΔΔG values for this last oxidation are consistent with previous experimental results, while regeneration within an alternative catalytic cycle was found to be thermodynamically unfavorable. Extensive in silico sampling of catalyst structures also revealed two degradation processes: cubane opening and ligand dissociation, both of which have low barriers at highly reduced states of the catalyst due to the presence of Jahn-Teller effects. These mechanistic insights are expected to spur the development of more efficient and stable Mn cubane water oxidation catalysts.

Group 13 salphen compounds (In, Ga and Al): a comparison of their structural features and activities as catalysts for cyclic carbonate synthesis

Many complexes based on group 13 elements have been successfully applied as catalysts for the synthesis of cyclic carbonates from epoxides and CO₂ and to date these have provided some of the most active catalysts developed. It is notable that most reports have focused on the use of aluminium-based compounds likely because of the well-established Lewis acidity of this element and its cost. In comparison, relatively little attention has been paid to the development of catalysts based on the heavier group 13 elements, despite their known Lewis acidic properties. This study describes the synthesis of aluminium, gallium and indium compounds supported by a readily prepared salphen ligand and explores both their comparative structures and also their potential as catalysts for the synthesis of cyclic carbonates. In addition, the halide ligand which forms a key part of the compound has been systematically varied and the effect of this change on the structure and catalytic activity is also discussed. It is demonstrated that the indium compounds are actually, and unexpectedly, the most active for cyclic carbonate synthesis, despite their lower Lewis acidity when compared to their aluminium congeners. The experimental observations from this work are fully supported by a Density Functional Theory (DFT) study, which provides important insights into the reasons as to why the indium catalyst with bromide, [InBr(salphen)], is most active.

Molecular Understanding and Practical In Silico Catalyst Design in Computational Organocatalysis and Phase Transfer Catalysis-Challenges and Opportunities

Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed.

The computational road to reactivity scales

Reactivity scales are useful research tools for chemists, both experimental and computational. However, to determine the reactivity of a single molecule, multiple measurements need to be carried out, which is a time-consuming and resource-intensive task. In this Tutorial Review, we present alternative approaches for the efficient generation of quantitative structure-reactivity relationships that are based on quantum chemistry, supervised learning, and uncertainty quantification. First published in 2002, we observe a tendency for these relationships to become not only more predictive but also more interpretable over time.

Solvent Coordination Effect on Copper-Based Molecular Catalysts for Controlled Radical Polymerization

The equilibrium of copper-catalyzed atom transfer radical polymerization was investigated in silico with the aim of finding an explanation for the experimentally observed solvent effect. Various combinations of alkyl halide initiators and copper complexes in acetonitrile (MeCN) and dimethyl sulfoxide (DMSO) were taken into consideration. A continuum model for solvation, which does not account for the explicit interactions between the solvent and metal complex, is not adequate and does not allow the reproduction of the experimental trend. However, when the solvent molecules are included in the coordination sphere of the copper(I,II) species and the continuum description of the medium is still used, a solvent dependence of process thermodynamics emerges, in fair agreement with experimental trends.

Encapsulation Enhances the Catalytic Activity of C-N Coupling: Reaction Mechanism of a Cu(I)/Calix[8]arene Supramolecular Catalyst

Development of C-N coupling methodologies based on Earth-abundant metals is a promising strategy in homogeneous catalysis for sustainable processes. However, such systems suffer from deactivation and low catalytic activity. We here report that encapsulation of Cu(I) within the phenanthroyl-containing calix[8]arene derivative 1,5-(2,9-dimethyl-1,10-phenanthroyl)-2,3,4,6,7,8-hexamethyl-p-tert-butylcalix[8]arene (C8PhenMe6 ) significantly enhances C-N coupling activity up to 92 % yield in the reaction of aryl halides and aryl amines, with low catalyst loadings (2.5 % mol). A tailored multiscale computational protocol based on Molecular Dynamics simulations and DFT investigations revealed an oxidative addition/reductive elimination process of the supramolecular catalyst [Cu(C8PhenMe6)I]. The computational investigations uncovered the origins of the enhanced catalytic activity over its molecular analogues: Catalyst deactivation through dimerization is prevented, and product release facilitated. Capturing the dynamic profile of the macrocycle and the impact of non-covalent interactions on reactivity allows for the rationalization of the behavior of the flexible supramolecular catalysts employed.

Best-Practice DFT Protocols for Basic Molecular Computational Chemistry

Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share of these quantum-chemical calculations applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on the numerous methodological and technical aspects of DFT calculations in three parts: Firstly, we set the stage and introduce a step-by-step decision tree to choose a computational protocol that models the experiment as closely as possible. Secondly, we present a recommendation matrix to guide the choice of functional and basis set depending on the task at hand. A particular focus is on achieving an optimal balance between accuracy, robustness, and efficiency through multi-level approaches. Finally, we discuss selected representative examples to illustrate the recommended protocols and the effect of methodological choices.

Mechanism of Coupling of Methylidene to Ethylene Ligands in Dimetallic Assemblies; Computational Investigation of a Model for a Key Step in Catalytic C1 Chemistry

Methylidene complexes often couple to ethylene complexes, but the mechanistic insight is scant. The path by which two cations [(η⁵-C₅H₅)Re(NO)(PPh₃)(═CH₂)]⁺ (5⁺) transform (CH₂Cl₂/acetonitrile) to [(η⁵-C₅H₅)Re(NO)(PPh₃)(H₂C═CH₂)]⁺ (6⁺) and [(η⁵-C₅H₅)Re(NO)(PPh₃)(NCCH₃)]⁺ is studied by density functional theory. Experiments provide a number of constraints such as the second-order rate in 5⁺; no prior ligand dissociation/exchange; a faster reaction of (S)-5⁺ with (S)-5⁺ than with (R)-5⁺ ("enantiomer self-recognition"). Although dirhenium dications with Re(μ-CH₂)₂Re cores represent energy minima, they are not accessible by 2 + 2 cycloadditions of 5⁺. Transition states leading to ReCH₂CH₂Re linkages are prohibitively high in energy. However, 5⁺ can give non-covalent S_Re/S_Re or S_Re/R_Re dimers with π interactions between the PPh₃ ligands but long ReCH₂···H₂CRe and H₂CRe···H₂CRe distances (3.073-3.095 Å and 3.878-4.529 Å, respectively). In rate-determining steps, these afford [(η⁵-C₅H₅)Re(NO)(PPh₃)(μ-η²:η²-H₂C···CH₂)(Ph₃P)(ON)Re(η⁵-C₅H₅)]²⁺ (13²⁺), in which one rhenium binds the bridging ethylene more tightly than the other (2.115-2.098 vs 2.431-2.486 Å to the centroid). In the S_Re/R_Re adduct, Dewar-Chatt-Duncanson optimization leads to unfavorable PPh₃/PPh₃ contacts. Ligand interactions are further dissected in the preceding transition states via component analyses, and ΔΔG^‡ (1.2 kcal/mol, CH₂Cl₂) favors the S_Re/S_Re pathway, in accordance with the experiment. Acetonitrile then displaces 6⁺ from the more weakly bound rhenium of 13²⁺. The formation of similar μ-H₂C···CH₂ intermediates is found to be rate-determining for varied coordinatively saturated M═CH₂ species [M = Fe(d⁶)/Re(d⁴)/Ta(d²)], establishing generality and enhancing relevancy to catalytic CH₄ and CO/H₂ chemistry.

Silyl Groups Are Strong Dispersion Energy Donors

We present an experimental and computational study to investigate noncovalent interactions between silyl groups that are often employed as "innocent" protecting groups. We chose an extended cyclooctatetraene (COT)-based molecular balance comprising unfolded (1,4-disubstituted) and folded (1,6-disubstituted) valance bond isomers that typically display remote and close silyl group contacts, respectively. The thermodynamic equilibria were determined using nuclear magnetic resonance measurements. Additionally, we utilized Boltzmann weighted symmetry-adapted perturbation theory (SAPT) at the sSAPT0/aug-cc-pVDZ level of theory to dissect and quantify noncovalent interactions. Apart from the extremely bulky tris(trimethylsilyl)silyl "supersilyl" group, there is a preference for the folded 1,6-COT valence isomer, with London dispersion interactions being the main stabilizing factor. This makes silyl groups excellent dispersion energy donors, a finding that needs to be taken into account in synthesis planning.

Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes

Volcano plots and activity maps are powerful tools for studying homogeneous catalysis. Once constructed, they can be used to estimate and predict the performance of a catalyst from one or more descriptor variables. The relevance and utility of these tools has been demonstrated in several areas of catalysis, with recent applications to homogeneous catalysts having been pioneered by our research group. Both volcano plots and activity maps are built from linear free energy scaling relationships that connect the value of a descriptor variable(s) with the relative energies of other catalytic cycle intermediates/transition states. These relationships must be both constructed and postprocessed appropriately to obtain the resulting plots/maps; this process requires careful execution to obtain meaningful results. In this protocol, we provide a step-by-step guide to building volcano plots and activity maps using curated reaction profile data. The reaction profile data are obtained using density functional theory computations to model the catalytic cycle. In addition, we provide volcanic, a Python code that automates the steps of the process following data acquisition. Unlike the computation of individual reaction energy profiles, our tools lead to a holistic view of homogeneous catalyst performance that can be broadly applied for both explanatory and screening purposes.

A Plausible Mechanism for the Iridium-Catalyzed Hydrogenation of a Bulky N-Aryl Imine in the (S)-Metolachlor Process

The hydrogenation of N-(2-ethyl-6-methylphenyl)-1-methoxypropan-2-imine is the largest-scale asymmetric catalytic process for the industrial production of agrochemical (S)-metolachlor. The challenging hydrogenation across the sterically crowded carbon–nitrogen double bond was achieved using a mixture of [IrCl(COD)]₂, (R,S_Fc)-Xyliphos, NBu₄I and acetic acid. Acetic acid was critical in achieving excellent productivity and activity. Despite its industrial significance, a mechanism that explains how the sterically hindered bond in the imine is reduced has yet to be proposed. We propose a plausible proton-first, outer-sphere mechanism based on density functional theory calculations that is consistent with the experimentally observed activity and the enantioselectivity of the industrial process. Key findings include transition states involving acetate-assisted dihydrogen splitting, and a hydride transfer from a five-coordinate iridium trihydride directed by a C-H∙∙∙Ir interaction. This article was submitted to a Special Issue in honor of Professor Henri Kagan.

Theoretical investigation on the reaction mechanism of UTP cyclohydrolase

Nucleoside triphosphate cyclohydrolase (UrcA) is a critical enzyme of the uracil catabolism pathway that catalyses the two-step hydrolysis of uridine triphosphate (UTP). Although the recently resolved X-ray structure of UrcA in complex with substrate analogue dUTP provided insights into the structural characteristics of the enzyme, the detailed catalytic mechanism, including how the reaction intermediate accomplishes conformational conversion in the active centre, remains unclear. In this study, extensive DFT calculations and MD simulations were performed to investigate the catalytic reaction process of UrcA. This study shows that the first hydrolytic reactions in UrcA follow a three-step mechanism, while the second hydrolytic reaction follows a two-step mechanism. Glu392 plays a critical role in deprotonating the lytic water in both hydrolytic reactions. The rate-limiting step of the first hydrolytic reaction lies in the cleavage of the uracil ring, in which an extraneous water molecule bridges the proton transfer from C6-OH to N1 to enable the reaction to go through a six-membered transition state with relatively low steric tension. In the second hydrolytic reaction, Glu392 abstracts protons from the lytic water and directly transfers them to the nitrogen atom of the cleaved C4-N3 bond so that the hydrolytic reaction is no longer rate-limited by the C-N bond cleavage step. MD simulations show that the reaction intermediate experiences spontaneous conformation overturn in the active site of UrcA under the assistance of the hydrogen bond interaction from Tyr307 to place its C4-N3 bond alongside the Zn2+ centre of the enzyme to trigger the second hydrolytic reaction.

Thermodynamics of metallocene catalyst activation: alignment of theory and experiment

Three equilibria involved in metallocene catalyst activation, including dissociation of R₆Al₂ (R = Me, Et or i-Bu) and related species such as [L₂ZrMe₂AlMe₂][B(C₆F₅)₄] (L₂ = Cp₂, 1,2-ethylenebis(η⁵-indenyl), Me₂C(η⁵-C₅H₄)₂) or [(L₂ZrMe)₂μ-Me][MePBB] (L₂ = (h⁵-1,2-Me₂C₅H₃)₂, [MePBB]^- = [MeB(Ar_F)₃]^- with Ar_F = o-C₆F₅-C₆F₄) are studied by DFT using various approaches to account for the enthalpy and entropy changes in gas and condensed phases. These studies reveal that both low energy vibrations and translational entropy conspire to cause significant deviations between theory and experiment when it comes to the free energy change in condensed or even gas phase. Alignment of theory with experiment requires in addition, consideration of specific solvation of reactants and products.

Increasing Complexity in a Conformer Space Step-by-Step: Weighing London Dispersion against Cation-π Interactions

We report an evaluation of the importance of London dispersion in moderately large (up to 36 heavy atoms) organic molecules by means of a molecular torsion balance whose conformations "weigh" one interaction against another in the absence of solvents. The experimental study, with gas-phase cryogenic ion vibrational predissociation (CIVP) spectroscopy, solid-state Fourier transfer infrared (FT-IR), and single-crystal X-ray crystallography, is accompanied by density functional theory calculations, including an extensive search and analysis of accessible conformations. We begin with the unsubstituted molecular torsion balance, and then step up the complexity systematically by adding alkyl groups incrementally as dispersion energy donors (DEDs) to achieve a degree of chemical complexity comparable to what is typically found in transition states for many regio- and stereoselective reactions in organic and organometallic chemistry. We find clear evidence for the small attractive contribution by DEDs, as had been reported in other studies, but we also find that small individual contributions by London dispersion, when they operate in opposition to other weak noncovalent interactions, produce composite effects on the structure that are difficult to predict intuitively, or by modern quantum chemical calculations. The experimentally observed structures, together with a reasonable value for a reference cation-π interaction, indicate that the pairwise interaction between two tert-butyl groups, in the best case, is modest. Moreover, the visualization of the conformational space, and comparison to spectroscopic indicators of the structure, as one steps up the complexity of the manifold of noncovalent interactions, makes clear that in silico predictive ability for the structure of moderately large, flexible, organic molecules falters sooner than one might have expected.

Salt-Enhanced Oxidative Addition of Iodobenzene to Pd: An Interplay Between Cation, Anion, and Pd-Pd Cooperative Effects

Halide salts facilitate the oxidative addition of organic halides to Pd(0). This phenomenon originates from a combination of anionic, cationic, and Pd-Pd cooperative effects. Exhaustive computational exploration at the density functional theory level of the complexes obtained from [Pd⁰(PPh₃)₂] and a salt (NMe₄Cl or LiCl) showed that chlorides promote phosphine release, leading to a mixture of mononuclear and dinuclear Pd(0) complexes. Anionic Pd(0) dinuclear complexes exhibit a cooperativity between Pd(0) centers, which favors the oxidative addition of iodobenzene. The higher activity of Pd(0) dimers toward oxidative addition rationalizes the previously reported kinetic laws. In the presence of Li⁺, the oxidative addition to mononuclear [Pd⁰L(Li₂Cl₂)] is estimated barrierless. LiCl coordination polarizes Pd(0), enlarging both the electrophilicity and the nucleophilicity of the complex, which promotes both coordination of the substrate and the subsequent insertion into the C-I bond. These conclusions are paving the way to the rational use of the salt effects in catalysis for the activation of more challenging bonds.

New Insights and Predictions into Complex Homogeneous Reactions Enabled by Computational Chemistry in Synergy with Experiments: Isotopes and Mechanisms

Homogeneous catalysis and biocatalysis have been widely applied in synthetic, medicinal, and energy chemistry as well as synthetic biology. Driven by developments of new computational chemistry methods and better computer hardware, computational chemistry has become an essentially indispensable mechanistic "instrument" to help understand structures and decipher reaction mechanisms in catalysis. In addition, synergy between computational and experimental chemistry deepens our mechanistic understanding, which further promotes the rational design of new catalysts. In this Account, we summarize new or deeper mechanistic insights (including isotope, dispersion, and dynamical effects) into several complex homogeneous reactions from our systematic computational studies along with subsequent experimental studies by different groups. Apart from uncovering new mechanisms in some reactions, a few computational predictions (such as excited-state heavy-atom tunneling, steric-controlled enantioswitching, and a new geminal addition mechanism) based on our mechanistic insights were further verified by ensuing experiments.The Zimmerman group developed a photoinduced triplet di-π-methane rearrangement to form cyclopropane derivatives. Recently, our computational study predicted the first excited-state heavy-atom (carbon) quantum tunneling in one triplet di-π-methane rearrangement, in which the reaction rates and ¹²C/¹³C kinetic isotope effects (KIEs) can be enhanced by quantum tunneling at low temperatures. This unprecedented excited-state heavy-atom tunneling in a photoinduced reaction has recently been verified by an experimental ¹²C/¹³C KIE study by the Singleton group. Such combined computational and experimental studies should open up opportunities to discover more rare excited-state heavy-atom tunneling in other photoinduced reactions. In addition, we found unexpectedly large secondary KIE values in the five-coordinate Fe(III)-catalyzed hetero-Diels-Alder pathway, even with substantial C-C bond formation, due to the non-negligible equilibrium isotope effect (EIE) derived from altered metal coordination. Therefore, these KIE values cannot reliably reflect transition-state structures for the five-coordinate metal pathway. Furthermore, our density functional theory (DFT) quasi-classical molecular dynamics (MD) simulations demonstrated that the coordination mode and/or spin state of the iron metal as well as an electric field can affect the dynamics of this reaction (e.g., the dynamically stepwise process, the entrance/exit reaction channels).Moreover, we unveiled a new reaction mechanism to account for the uncommon Ru(II)-catalyzed geminal-addition semihydrogenation and hydroboration of silyl alkynes. Our proposed key gem-Ru(II)-carbene intermediates derived from double migrations on the same alkyne carbon were verified by crossover experiments. Additionally, our DFT MD simulations suggested that the first hydrogen migration transition-state structures may directly and quickly form the key gem-Ru-carbene structures, thereby "bypassing" the second migration step. Furthermore, our extensive study revealed the origin of the enantioselectivity of the Cu(I)-catalyzed 1,3-dipolar cycloaddition of azomethine ylides with β-substituted alkenyl bicyclic heteroarenes enabled by dual coordination of both substrates. Such mechanistic insights promoted our computational predictions of the enantioselectivity reversal for the corresponding monocyclic heteroarene substrates and the regiospecific addition to the less reactive internal C═C bond of one diene substrate. These predictions were proven by our experimental collaborators. Finally, our mechanistic insights into a few other reactions are also presented. Overall, we hope that these interactive computational and experimental studies enrich our mechanistic understanding and aid in reaction development.

Solvent-mediated outer-sphere CO2 electro-reduction mechanism over the Ag111 surface

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.

Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis

Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to catalysis: (i) automation allows one to consider orders of magnitude more structures in a systematic and open-ended fashion than what would be accessible by manual inspection. Eventually, full resolution in terms of structural varieties and conformations as well as with respect to the type and number of potentially important elementary reaction steps (including decomposition reactions that determine turnover numbers) may be achieved. (ii) Fast electronic structure methods with uncertainty quantification warrant high efficiency and reliability in order to not only deliver results quickly, but also to allow for predictive work. (iii) A high degree of autonomy reduces the amount of manual human work, processing errors, and human bias. Although being inherently unbiased, it is still steerable with respect to specific regions of an emerging network and with respect to the addition of new reactant species. This allows for a high fidelity of the formalization of some catalytic process and for surprising in silico discoveries. In this work, we first review the state of the art in computational catalysis to embed autonomous explorations into the general field from which it draws its ingredients. We then elaborate on the specific conceptual issues that arise in the context of autonomous computational procedures, some of which we discuss at an example catalytic system.

Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II

Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol^-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol^-1 can be inferred for the known k_cat ≈ 1 s^-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (k_cat = 8.6 × 10^-5 s^-1 to 2.7 s^-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH^⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.

Electronic structure analysis of electrochemical CO2 reduction by iron-porphyrins reveals basic requirements to design catalysts bearing non-innocent ligands

Electrocatalytic CO2 reduction is a possible solution to the increasing CO2 concentration in the earth atmosphere, because it enables storage of energy while using the harmful CO2 feedstock as starting...

Blue light enhanced Heck arylation at room temperature applied to allenes

A blue light enhanced synthesis of 2-vinyl pirrolidines and piperidines through a domino Heck arylation–cyclisation applied to allenyl amines is described. Essential is the role of the light in the aryl migration in the carbo-palladation step.

A comparative study of Rh2-catalyzed intermolecular nitrene transfer reactions: mechanism and chemoselectivity

The intermolecular catalytic mechanisms using Rh2(esp)2 and Rh2(OAc)4 are analogous and their large difference in aziridination-to-amination chemoselectivity stems from the steric effect.

The (not so) simple prediction of enantioselectivity – a pipeline for high-fidelity computations

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.

The computation of reaction selectivity represents an appealing complementary route to experimental studies and a powerful mean to refine catalyst design strategies.

DFT study on the gold(I)-catalyzed cycloaddition and rearrangement reactions of allene-containing allylic silyl ether

The DFT calculation at the B3LYP/B3LYP-D3(BJ) level was carried out to explore the reaction mechanism of the synthesis of spirocyclo[4,5]decane skeleton by gold-catalyzed allenyl compounds. The more accurate energy under the CH₃CN solvent in the experiment is calculated by the single-point energy of the SMD model. Computational studies have shown that the reaction consists of three main steps: intramolecular cycloaddition of the end group carbon atoms of allenyl and vinyl groups, the semipinacol rearrangement process in which the four-membered ring is reconstructed into the five-membered ring, the elimination reaction releases the catalyst and obtains the product. The calculation results show that Zheng et al. reported that the gold-catalyzed synthesis reaction can easily occur under the experimental conditions due to its low activation free energy (12.07-15.49 kcal/mol). Furthermore, it was found that the MOMO(CH₂)₂ substituent has higher reactivity than the corresponding reactant of the phenyl substituent.

Heavy-Atom Kinetic Isotope Effects: Primary Interest or Zero Point?

Chemists have many options for elucidating reaction mechanisms. Global kinetic analysis and classic transition-state probes (e.g., LFERs, Eyring) inevitably form the cornerstone of any strategy, yet their application to increasingly sophisticated synthetic methodologies often leads to a wide range of indistinguishable mechanistic proposals. Computational chemistry provides powerful tools for narrowing the field in such cases, yet wholly simulated mechanisms must be interpreted with great caution. Heavy-atom kinetic isotope effects (KIEs) offer an exquisite but underutilized method for reconciling the two approaches, anchoring the theoretician in the world of calculable observables and providing the experimentalist with atomistic insights. This Perspective provides a personal outlook on this synergy. It surveys the computation of heavy-atom KIEs and their measurement by NMR spectroscopy, discusses recent case studies, highlights the intellectual reward that lies in alignment of experiment and theory, and reflects on the changes required in chemical education in the area.

Computational Analysis of a Prebiotic Amino Acid Synthesis with Reference to Extant Codon-Amino Acid Relationships

Novel density functional theory calculations are presented regarding a mechanism for prebiotic amino acid synthesis from alpha-keto acids that was suggested to happen via catalysis by dinucleotide species. Our results were analysed with comparison to the original hypothesis (Copley et al., PNAS, 2005, 102, 4442–4447). It was shown that the keto acid–dinucleotide hypothesis for possible prebiotic amino acid synthesis was plausible based on an initial computational analysis, and details of the structures for the intermediates and transition states showed that there was wide scope for interactions between the keto acid and dinucleotide moieties that could affect the free energy profiles and lead to the required proto-metabolic selectivity.