Theory and modeling of stereoselective organic reactions

The Cambridge Structural Database and structural dynamics

With the availability of the computer readable information in the Cambridge Structural Database (CSD), wide ranging, largely automated comparisons of fragment, molecular, and crystal structures have become possible. They show that the distributions of interatomic distances, angles, and torsion angles for a given structural fragment occurring in different environments are highly correlated among themselves and with other observables such as spectroscopic signals, reaction and activation energies. The correlations often extend continuously over large ranges of parameter values. They are reminiscent of bond breaking and forming reactions, polyhedral rearrangements, and conformational changes. They map-qualitatively-the regions of the structural parameter space in which molecular dynamics take place, namely, the low energy regions of the respective (free) energy surfaces. The extension and continuous nature of the correlations provides an organizing principle of large groups of structural data and suggests a reconsideration of traditional definitions and descriptions of bonds, "nonbonded" and "noncovalent" interactions in terms of Lewis acids interacting with Lewis bases. These aspects are illustrated with selected examples of historic importance and with some later developments. It seems that the amount of information in the CSD (and other structural databases) and the knowledge on the nature of, and the correlations within, this body of information should allow one-in the near future-to make credible interpolations and possibly predictions of structures and their properties with machine learning methods.

Experimental and theoretical elucidation of SPAAC kinetics for strained alkyne-containing cycloparaphenylenes

Tuning strained alkyne reactivity via organic synthesis has evolved into a burgeoning field of study largely focused on cyclooctyne, wherein physical organic chemistry helps guide rational molecular design to produce molecules with intriguing properties. Concurrent research in the field of carbon nanomaterials has produced new types of strained alkyne macrocycles, such as cycloparaphenyleneacetylenes, that possess uniquely curved aromatic π systems but hover on the edge of stability. In 2018, we introduced a strained alkyne scaffold that marries the synthetic accessibility and stability of cyclooctyne with the curved π system of carbon nanomaterials. These molecules are strained alkyne-containing cycloparaphenylenes (or [n+1]CPPs), which have been shown to possess size-dependent reactivity as well as the classic characteristics of the unfunctionalized parent CPP, such as a tunable HOMO-LUMO gap and bright fluorescence for large sizes. Herein, we elaborate further on this scaffold, introducing two modifications to the original design and fully characterizing the kinetics of the strain-promoted azide-alkyne cycloaddition (SPAAC) for each [n+1]CPP with a model azide. Additionally, we explain how electronic (the incorporation of fluorine atoms) and strain (a meta linkage which heightens local strain at the alkyne) modulations affect SPAAC reactivity via the distortion-interaction computational model. Altogether, these results indicate that through a modular synthesis and rational chemical design, we have developed a new family of tunable and inherently fluorescent strained alkyne carbon nanomaterials.

Computational investigation of the radical-mediated mechanism of formation of difluoro methyl oxindoles: Elucidation of the reaction selectivity and yields

Oxindoles are an important class of heterocyclic alkaloids with demonstrated pharmacological activity at multiple biological targets. Preparation of new analogs through novel synthetic routes is therefore highly attractive. In this work, we report a computational study to investigate the synthesis of ethoxycarbonyldifluoromethylated oxindoles from N-arylmethacrylamides. The reaction tolerates a diverse range of acrylamides, shows yields ranging from approximately 38%-96%. We have applied density functional theory (DFT) to explore the reaction mechanism, kinetics and thermodynamics to gain further understanding. We demonstrate that a radical-based ring closure reaction is energetically more favorable than a heterolytic process, that the rate-determining step is the formation of the arylmethacrylamide radical, and that the product yields and selectivities are consistent with experiment. The results demonstrate that theoretical methods can prove useful to understand how such reaction and could be potentially employed to rapidly explore the reaction scope further.

Machine learning and semi-empirical calculations: a synergistic approach to rapid, accurate, and mechanism-based reaction barrier prediction

Modern QM modelling methods, such as DFT, have provided detailed mechanistic insights into countless reactions. However, their computational cost inhibits their ability to rapidly screen large numbers of substrates and catalysts in reaction discovery. For a C-C bond forming nitro-Michael addition, we introduce a synergistic semi-empirical quantum mechanical (SQM) and machine learning (ML) approach that allows the prediction of DFT-quality reaction barriers in minutes, even on a standard laptop using widely available modelling software. Mean absolute errors (MAEs) are obtained that are below the accepted chemical accuracy threshold of 1 kcal mol-1 and substantially better than SQM methods without ML correction (5.71 kcal mol-1). Predictive power is shown to hold when the ML models are applied to an unseen set of compounds from the toxicology literature. Mechanistic insight is also achieved via the generation of full SQM transition state (TS) structures which are found to be very good approximations for the DFT-level geometries, revealing important steric interactions in some TSs. This combination of speed, accuracy, and mechanistic insight is unprecedented; current ML barrier models compromise on at least one of these important criteria.

Identifying the true origins of selectivity in chiral phosphoric acid catalyzed N-acyl-azetidine desymmetrizations

The first catalytic intermolecular desymmetrization of azetidines was reported by Sun and coworkers in 2015 using a BINOL-derived phosphoric acid catalyst (J. Am. Chem. Soc. 2015, 137, 5895-5898). To uncover the mechanism of the reaction and the origins of the high enantioselectivity, Density Functional Theory (DFT) calculations were performed at the B97D3/6-311+G(2d,2p)/SMD(toluene)//B97D3/6-31G(d,p)/CPCM(toluene) level of theory. Comparison of four possible activation modes confirms that this reaction proceeds through the bifunctional activation of the azetidine nitrogen and the thione tautomer of the 2-mercaptobenzothiazole nucleophile. Upon thorough conformational sampling of the enantiodetermining transition structures (TSs), a free energy difference of 2.0 kcal mol-1 is obtained, accurately reproducing the experimentally measured 88% e.e. at 80 °C. This energy difference is due to both decreased distortion and increased non-covalent interactions in the pro-(S) TS. To uncover the true origins of selectivity, the TSs optimized with the full catalyst were compared to those optimized with a model catalyst through steric maps. It is found that the arrangements displayed by the substrates are controlled by strict primary orbital interaction requirements at the transition complex, and their ability to fit into the catalyst pocket drives the selectivity. A general model of selectivity for phosphoric acid-catalyzed azetidine desymmetrizations is proposed, which is based on the preference of the nucleophile and benzoyl group to occupy empty quadrants of the chiral catalyst pocket.

Teaching a neural network to attach and detach electrons from molecules

Interatomic potentials derived with Machine Learning algorithms such as Deep-Neural Networks (DNNs), achieve the accuracy of high-fidelity quantum mechanical (QM) methods in areas traditionally dominated by empirical force fields and allow performing massive simulations. Most DNN potentials were parametrized for neutral molecules or closed-shell ions due to architectural limitations. In this work, we propose an improved machine learning framework for simulating open-shell anions and cations. We introduce the AIMNet-NSE (Neural Spin Equilibration) architecture, which can predict molecular energies for an arbitrary combination of molecular charge and spin multiplicity with errors of about 2-3 kcal/mol and spin-charges with error errors ~0.01e for small and medium-sized organic molecules, compared to the reference QM simulations. The AIMNet-NSE model allows to fully bypass QM calculations and derive the ionization potential, electron affinity, and conceptual Density Functional Theory quantities like electronegativity, hardness, and condensed Fukui functions. We show that these descriptors, along with learned atomic representations, could be used to model chemical reactivity through an example of regioselectivity in electrophilic aromatic substitution reactions.

Emerging computational approaches for the study of regio- and stereoselectivity in organic synthesis

Computational chemistry has become important in organic synthesis as it provides a detailed understanding of molecular structures and properties and detailed reaction mechanisms.

Predicting glycosylation stereoselectivity using machine learning

Predicting the stereochemical outcome of chemical reactions is challenging in mechanistically ambiguous transformations. The stereoselectivity of glycosylation reactions is influenced by at least eleven factors across four chemical participants and temperature. A random forest algorithm was trained using a highly reproducible, concise dataset to accurately predict the stereoselective outcome of glycosylations. The steric and electronic contributions of all chemical reagents and solvents were quantified by quantum mechanical calculations. The trained model accurately predicts stereoselectivities for unseen nucleophiles, electrophiles, acid catalyst, and solvents across a wide temperature range (overall root mean square error 6.8%). All predictions were validated experimentally on a standardized microreactor platform. The model helped to identify novel ways to control glycosylation stereoselectivity and accurately predicts previously unknown means of stereocontrol. By quantifying the degree of influence of each variable, we begin to gain a better general understanding of the transformation, for example that environmental factors influence the stereoselectivity of glycosylations more than the coupling partners in this area of chemical space.

Synthesis of (+)-Hypoxylactone through Allenoate γ-Addition: Revision of Stereochemistry

A synthesis of (+)-hypoxylactone has been accomplished in four steps starting from the allenoate γ-addition of threo-3-chloro-2-silyoxybutanals, leading to the revision of stereochemistry. The key was the discovery of control elements required to matching/mismatching cases in the allenoate γ-addition to provide the desired adducts as a single isomer. The utility of the γ-adduct was demonstrated with the Au(I)-catalyzed cyclization to afford (+)-xylogiblactone A. Use of Ag₂O was the key to epoxidation for preventing epimerization of the γ-lactone ring.

Efficient Computation of Free Energy Contributions for Association Reactions of Large Molecules

Modern density functional theory (DFT) methods are capable of providing accurate association energies for supramolecular systems and even protein-ligand complexes. However, the calculation of the essential harmonic vibrational frequencies needed to obtain free energies is often too computationally demanding. In this work, the corresponding thermostatistical contributions are computed in the well-established (modified) rigid-rotor-harmonic-oscillator approximation with structures and frequencies taken from low-cost quantum chemical methods, namely, GFN2-xTB and PM6-D3H4. Additionally, a recently developed new general force field (GFN-FF) is tested for this purpose. DFT reference values for 59 complexes composed of three standard noncovalent and supramolecular benchmark sets (S22, L7, and S30L) are used in the evaluation. Overall, the accuracy of the low-cost methods is remarkable with typical deviations of only 0.5-2 kcal mol^-1 (5-10%) from the DFT reference values. In particular, the performance of the GFN-FF is promising considering the acceleration of 5 and 2-3 orders of magnitude compared to DFT and GFN2-xTB, respectively. This opens new perspectives for computing thermodynamic properties of, e.g., biomacromolecules as shown, for example, for the binding of retinol and rivaroxaban in protein complexes consisting of ≤4700 atoms.

Stereoselective gridization and polygridization with centrosymmetric molecular packing

The gridarenes, with well-defined edges and vertices, represent versatile nanoscale building blocks for the installation of frameworks and architectures but suffer from difficulty in stereoselective control during their synthesis. Here we report a diastereoselective gridization of superelectrophilic diazafluorene-containing substrates (A_mB_n) with crescent shapes into Drawing Hands grids (DHGs). The meso-selectivity reaches 75.6% diastereomeric excess (de) during the gridization of A₁B₁-type substrates and maintains ~80% de during the polygridization of A₂B₂-type monomers. Such stereocontrol originates from the centrosymmetric molecular packing of two charge-delocalized superelectrophiles with synergistically π–π stacking attractions and coulombic repulsions. As meso-stereoregular structures show 20∼30 nm in length, the rigid ring/chain-alternating polygrids have a Mark–Houwink exponent of 1.651 and a molecular weight (M) dependence of the hydrodynamic radius R_h ∼ M^1.13. Via the simulation of chain collapse, meso-configured polygridarenes still adopt rod-like conformations that facilitate the high rigidity of organic nanopolymers, distinguished from toroid backbones of rac-type polygrids.

Gridarenes with well-defined edges and vertices represent versatile nanoscale building blocks for installating frameworks but suffer from lack of stereoselective control during their synthesis. Here, the authors report a diastereoselective gridization of superelectrophilic diazafluorene-containing substrates with crescent shapes into Drawing Hands grids (DHGs).

Kinetic Resolution of Racemic Aldehydes through Asymmetric Allenoate γ-Addition: Synthesis of (+)-Xylogiblactone A

A synthesis of (+)-xylogiblactone A has been achieved from t-butyl 2-methylbuta-2,3-dienoate in a linear three-step sequence. The key elements of the synthesis include a kinetic resolution of racemic 2-silyoxyaldehyde through the allenoate γ-addition to yield the γ-adduct as a single isomer and the subsequent gold catalysis to form the butenolide core. For a general method, the kinetic resolution of several racemic 2-silyloxyaldehydes is also performed to provide products in high levels of stereoselectivity with unusual anti-Felkin-Anh addition fashion.

Mechanistic understanding of catalysis by combining mass spectrometry and computation

The combination of mass spectrometry and computational chemistry has been proven to be powerful for exploring reaction mechanisms. The former provides information of reaction intermediates, while the latter gives detailed reaction energy profiles.

Total Synthesis of (-)-Chromodorolide B By a Computationally-Guided Radical Addition/Cyclization/Fragmentation Cascade

The first total synthesis of a chromodorolide marine diterpenoid is described. The core of the diterpenoid is constructed by a bimolecular radical addition/cyclization/fragmentation cascade that unites two complex fragments and forms two C-C bonds and four contiguous stereogenic centers of (-)-chromodorolide B in a single step. This coupling step is initiated by visible-light photocatalytic fragmentation of a redox-active ester, which can be accomplished in the presence of an iridium or a less-precious electron-rich dicyanobenzene photocatalyst, and employs equimolar amounts of the two addends. Computational studies guided the development of this central step of the synthesis and provide insight into the origin of the observed stereoselectivity.

Chiral Phosphoric Acid Catalyzed Enantioselective Ring Expansion Reaction of 1,3-Dithiane Derivatives: Case Study of the Nature of Ion-Pairing Interaction

Chiral counterion controlled asymmetric catalysis via an ion-pairing interaction has attracted immense attention in recent years. Despite a number of successful studies, the mechanistic elucidation of the stereocontrolling element in the ion-pairing interaction is rarely conducted and hence its nature is still far from being well understood. Herein we report an in-depth mechanistic case study of a newly developed enantioselective ring expansion reaction of 1,3-dithiane derivatives catalyzed by chiral phosphoric acid (CPA). An unprecedented enantioselective 1,2-sulfur rearrangement/stereospecific nucleophilic addition sequence was proven to be the stereoselective pathway. More importantly, by thorough investigation of the intrinsic nature of the stereospecific nucleophilic addition to the cationic thionium intermediate, we discovered that the key interaction in this process is the nonclassical C-H···O hydrogen bonds formed between the conjugate base of the CPA catalyst and the cationic intermediate. These C-H···O hydrogen bonds not only bind the catalyst to the substrates to form energetically favored states throughout the overall processes but also firmly maintain the relative positions of these fragments as the "fixed" contact ion pair to sustain the chiral information generated at the initial sulfur rearrangement step. This mechanistic case study provides a very clear understanding of the nature of the ion-pairing interaction in organocatalysis. The conclusion encourages the further development of the research field with the focus to design new organocatalysts and cultivate novel organocatalytic transformations.

The stereodivergent formation of 2,6-cis and 2,6-trans-tetrahydropyrans: experimental and computational investigation of the mechanism of a thioester oxy-Michael cyclization

Computational and synthetic studies have elucidated the origins of stereodivergence in an oxy-Michael synthesis of 2,6-disubstituted tetrahydropyrans.

The origins of the stereodivergence in the thioester oxy-Michael cyclization for the formation of 4-hydroxy-2,6-cis- or 2,6-trans-substituted tetrahydropyran rings under different conditions was investigated both computationally and experimentally. Synthetic studies showed that the 4-hydroxyl group was essential for stereodivergence. When the 4-hydroxyl group was present, TBAF-mediated conditions gave the 2,6-trans-tetrahydropyran and trifluoroacetic acid-mediated conditions gave the 2,6-cis-tetrahydropyran. This stereodivergence vanished when the hydroxyl group was removed or protected. Computational studies revealed that: (i) the trifluoroacetic acid catalysed formation of 2,6-cis-tetrahydropyrans was mediated by a trifluoroacetate-hydroxonium bridge and proceeded via a chair-like transition state; (ii) the TBAF-mediated formation of 2,6-trans-tetrahydropyrans proceeded via a boat-like transition state, where the 4-hydroxyl group formed a crucial hydrogen bond to the cyclizing alkoxide; (iii) both reactions are under kinetic control. The utility of this stereodivergent approach for the formation of 4-hydroxy-2,6-substituted tetrahydropyran rings has been demonstrated by the total syntheses of the anti-osteoporotic natural products diospongin A and B.

New Mechanistic Insights on the Selectivity of Transition-Metal-Catalyzed Organic Reactions: The Role of Computational Chemistry

With new advances in theoretical methods and increased computational power, applications of computational chemistry are becoming practical and routine in many fields of chemistry. In organic chemistry, computational chemistry plays an indispensable role in elucidating reaction mechanisms and the origins of various selectivities, such as chemo-, regio-, and stereoselectivities. Consequently, mechanistic understanding improves synthesis and assists in the rational design of new catalysts. In this Account, we present some of our recent works to illustrate how computational chemistry provides new mechanistic insights for improvement of the selectivities of several organic reactions. These examples include not only explanations for the existing experimental observations, but also predictions which were subsequently verified experimentally. This Account consists of three sections discuss three different kinds of selectivities. The first section discusses the regio- and stereoselectivities of hydrosilylations of alkynes, mainly catalyzed by [Cp*Ru(MeCN)3](+) or [CpRu(MeCN)3](+). Calculations suggest a new mechanism that involves a key ruthenacyclopropene intermediate. This mechanism not only explains the unusual Markovnikov regio-selectivity and anti-addition stereoselectivity observed by Trost and co-workers, but also motivated further experimental investigations. New intriguing experimental observations and further theoretical studies led to an extension of the reaction mechanism. The second section includes three cases of meta-selective C-H activation of aryl compounds. In the case of Cu-catalyzed selective meta-C-H activation of aniline, a new mechanism that involves a Cu(III)-Ar-mediated Heck-like transition state, in which the Ar group acts as an electrophile, was proposed. This mechanism predicted a higher reactivity for more electron-deficient Ar groups, which was supported by experiments. For two template-mediated, meta-selective C-H bond activations catalyzed by Pd(II), different mechanisms were derived for the two templates. One involves a dimeric Pd-Pd or Pd-Ag active catalyst, and the other involves a monomeric Pd catalyst, in which a monoprotected amino acid coordinates in a bidentate fashion and serves as an internal base for C-H activation. The third section discusses a desymmetry strategy in asymmetric synthesis. The construction of rigid skeletons is critical for these catalysts to distinguish two prochiral groups. Overall, fruitful collaborations between computational and experimental chemists have provided new and comprehensive mechanistic understanding and insights into these useful reactions.

Theory and Modeling of Asymmetric Catalytic Reactions

Modern density functional theory and powerful contemporary computers have made it possible to explore complex reactions of value in organic synthesis. We describe recent explorations of mechanisms and origins of stereoselectivities with density functional theory calculations. The specific functionals and basis sets that are routinely used in computational studies of stereoselectivities of organic and organometallic reactions in our group are described, followed by our recent studies that uncovered the origins of stereocontrol in reactions catalyzed by (1) vicinal diamines, including cinchona alkaloid-derived primary amines, (2) vicinal amidophosphines, and (3) organo-transition-metal complexes. Two common cyclic models account for the stereoselectivity of aldol reactions of metal enolates (Zimmerman-Traxler) or those catalyzed by the organocatalyst proline (Houk-List). Three other models were derived from computational studies described in this Account. Cinchona alkaloid-derived primary amines and other vicinal diamines are venerable asymmetric organocatalysts. For α-fluorinations and a variety of aldol reactions, vicinal diamines form enamines at one terminal amine and activate electrophilically with NH(+) or NF(+) at the other. We found that the stereocontrolling transition states are cyclic and that their conformational preferences are responsible for the observed stereoselectivity. In fluorinations, the chair seven-membered cyclic transition states is highly favored, just as the Zimmerman-Traxler chair six-membered aldol transition state controls stereoselectivity. In aldol reactions with vicinal diamine catalysts, the crown transition states are favored, both in the prototype and in an experimental example, shown in the graphic. We found that low-energy conformations of cyclic transition states occur and control stereoselectivities in these reactions. Another class of bifunctional organocatalysts, the vicinal amidophosphines, catalyzes the (3 + 2) annulation reaction of allenes with activated olefins. Stereocontrol here is due to an intermolecular hydrogen bond that activates the electrophilic partner in this reaction. We have also studied complex organometallic catalysts. Krische's ruthenium-catalyzed asymmetric hydrohydroxyalkylation of butadiene involves two chiral ligands at Ru, a chiral diphosphine and a chiral phosphate. The size of this combination strains the limits of modern computations with over 160 atoms, multiple significant steps, and a variety of ligand coordinations and conformations possible. We found that carbon-carbon bond formation occurs via a chair Zimmerman-Traxler-type transition structure and that a formyl CH···O hydrogen bond from aldehyde CH to phosphate oxygen, as well as steric interactions of the two chiral ligands, control the stereoselectivity.

Development of a True Transition State Force Field from Quantum Mechanical Calculations

Transition state force fields (TSFF) treated the TS structure as an artificial minimum on the potential energy surface in the past decades. The necessary parameters were developed either manually or by the Quantum-to-molecular mechanics method (Q2MM). In contrast with these approaches, here we propose to model the TS structures as genuine saddle points at the molecular mechanics level. Different methods were tested on small model systems of general chemical reactions such as protonation, nucleophilic attack, and substitution, and the new procedure led to more accurate models than the Q2MM-type parametrization. To demonstrate the practicality of our approach, transferrable parameters have been developed for Mo-catalyzed olefin metathesis using quantum mechanical properties as reference data. Based on the proposed strategy, any force field can be extended with true transition state force field (TTSFF) parameters, and they can be readily applied in several molecular mechanics programs as well.

Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions

Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.

Torsional Control of Stereoselectivities in Electrophilic Additions and Cycloadditions to Alkenes

Torsional effects control the π-facial stereoselectivities of a variety of synthetically important organic reactions. This review surveys theoretical calculations that have led to the understanding of the influence of the torsional effects on several types of stereoselective organic reactions, especially electrophilic additions and cycloadditions to alkenes.

Increasing the efficiency of the transannular Diels-Alder strategy via palladium(II)-catalyzed macrocyclizations

Palladium(II)-catalyzed macrocyclizations of bis(vinylboronate ester) compounds are demonstrated to provide a strategically efficient approach to transannular Diels-Alder reaction substrates. In several systems reported, the macrocycle is preorganized such that cycloaddition at room temperature occurs concomitantly with cyclization. Numerous advantages over palladium(0)-catalyzed cross-coupling approaches are demonstrated.

H12461. Fluorine as a Regiocontrol Element in the Ring Openings of Bicyclic Aziridiniums

The origin of the variation in the regioselectivity of the nucleophilic ring-opening of a series of bicyclic aziridinium ions derived from N-alkylprolinols was investigated by quantum chemical computations (M06-2X/6-31+G(d,p)-SMD). These aziridiniums differ only in the degree and the stereochemistry of fluoro substitution at C(4). With the azide ion as nucleophile, the ratio of the piperidine to the pyrrolidine product was computed. An electrostatic gauche effect influences the conformation of the adjoining five-membered ring in the fluorinated bicyclic aziridinium. This controls the regioselectivity of the aziridinium ring-opening.

Origins of stereoselectivities of dihydroxylations of cis-bicyclo[3.3.0]octenes

Stereoselectivities of the dihydroxylations of cis-bicyclo[3.3.0]octene intermediates for a projected total synthesis of chromodorolide A have been explored experimentally. The reaction occurs unexpectedly on the apparently more hindered (concave) face; this result has been explained through computational studies using B3LYP and B3LYP-D3 methods. Torsional effects are largely responsible for the stereoselectivity encountered in the chromodorolide A synthesis. Many literature examples have been reported on related cases. QM calculations show that the stereoselectivities of dihydroxylations of fused cyclopentenes are influenced by the conformational rigidity or flexibility of the substrate. Torsional, electrostatic, and steric effects can all influence stereoselectivity, and the rigidity or flexibility of conformations of reactants provides a predictive guide to stereoselectivity.