Understanding the 1,3-Dipolar Cycloadditions of Allenes

Retro-Cope elimination of cyclic alkynes: reactivity trends and rational design of next-generation bioorthogonal reagents

The retro-Cope elimination reaction between dimethylhydroxylamine (DMHA) and various cyclic alkynes has been quantum chemically explored using DFT at ZORA-BP86/TZ2P. The purpose of this study is to understand the role of the following three unique activation modes on the overall reactivity, that is (i) additional cycloalkyne predistortion via fused cycles, (ii) exocyclic heteroatom substitution on the cycloalkyne, and (iii) endocyclic heteroatom substitution on the cycloalkyne. Trends in reactivity are analyzed and explained by using the activation strain model (ASM) of chemical reactivity. Based on our newly formulated design principles, we constructed a priori a suite of novel bioorthogonal reagents that are highly reactive towards the retro-Cope elimination reaction with DMHA. Our findings offer valuable insights into the design principles for highly reactive bioorthogonal reagents in chemical synthesis.

Density Functional Theory Calculations: A Useful Tool to Investigate Mechanisms of 1,3-Dipolar Cycloaddition Reactions

The present review contains a representative sampling of mechanistic studies, which have appeared in the literature in the last 5 years, on 1,3-dipolar cycloaddition reactions, using DFT calculations. Attention is focused on the mechanistic insights into 1,3-dipoles of propargyl/allenyl type and allyl type such as aza-ylides, nitrile oxides and azomethyne ylides and nitrones, respectively. The important role played by various metal-chiral-ligand complexes and the use of chiral eductors in promoting the site-, regio-, diastereo- and enatioselectivity of the reaction are also outlined.

Is DFT Accurate Enough to Calculate Regioselectivity? The Case of 1,3-Dipolar Cycloaddition of Azide to Alkynes and Alkenes

The importance of regioselectivity in 1,3-dipolar cycloadditions (DCs) makes it surprising that no benchmarking study on this problem has appeared. We investigated whether DFT calculations are an accurate tool to predict the regioselectivity of uncatalyzed thermal azide 1,3-DCs. We considered the reaction between HN3 and 12 dipolarophiles, comprising ethynes HC≡C-R and ethenes H2 C=CH-R (R=F, OH, NH2 , Me, CN, CHO), which cover a broad range of electron demand and conjugation ability. We established benchmark data by the W3X protocol [complete-basis-set-extrapolated CCSD(T)-F12 energy with T-(T) and (Q) corrections and MP2-calculated core/valence and relativistic effects] and showed that core/valence effects and high-order excitations are important for accurate regioselectivity. Regioselectivities calculated using an extensive set of density functional approximations (DFAs) were compared with benchmark data. Range-separated and meta-GGA hybrids gave the best results. Good treatment of self-interaction and electron exchange are the key features for accurate regioselectivity. Dispersion correction slightly improves agreement with W3X results. The best DFAs provide the isomeric TS energy difference with an expected error ≈0.7 mh and errors ≈2 mh can occur. The isomer yield provided by the best DFA has an expected error of ±5 %, though errors up to 20 % are not rare. At present, an accuracy of 1-2 % is unfeasible but it seems that we are not far from achieving this goal.

How Bases Catalyze Diels-Alder Reactions

We have quantum chemically studied the base-catalyzed Diels-Alder (DA) reaction between 3-hydroxy-2-pyrone and N-methylmaleimide using dispersion-corrected density functional theory. The uncatalyzed reaction is slow and is preceded by the extrusion of CO₂ via a retro-DA reaction. Base catalysis, for example, by triethylamine, lowers the reaction barrier up to 10 kcal mol^-1 , causing the reaction to proceed smoothly at low temperature, which quenches the expulsion of CO₂ , yielding efficient access to polyoxygenated natural compounds. Our activation strain analyses reveal that the base accelerates the DA reaction via two distinct electronic mechanisms: i) by the HOMO-raising effect, which enhances the normal electron demand orbital interaction; and ii) by donating charge into 3-hydroxy-2-pyrone which accumulates in its reactive region and promotes strongly stabilizing secondary electrostatic interactions with N-methylmaleimide.

The 1,3-Dipolar Cycloaddition: From Conception to Quantum Chemical Design

The 1,3-dipolar cycloaddition (1,3-DCA) reaction, conceptualized by Rolf Huisgen in 1960, has proven immensely useful in organic, material, and biological chemistry. The uncatalyzed, thermal transformation is generally sluggish and unselective, but the reactivity can be enhanced by means of metal catalysis or by the introduction of either predistortion or electronic tuning of the dipolarophile. These promoted reactions generally go with a much higher reactivity, selectivity, and yields, often at ambient temperatures. The rapid orthogonal reactivity and compatibility with aqueous and physiological conditions positions the 1,3-DCA as an excellent bioorthogonal reaction. Quantum chemical calculations have been critical for providing an understanding of the physical factors that control the reactivity and selectivity of 1,3-DCAs. In silico derived design principles have proven invaluable for the design of new dipolarophiles with tailored reactivity. This review discusses everything from the conception of the 1,3-DCA all the way to the state-of-the-art methods and models used for the quantum chemical design of novel (bioorthogonal) reagents.

Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance

Hierarchical, convergent ab initio benchmark computations were performed followed by a systematic analysis of DFT performance for five pericyclic reactions comprising Diels-Alder, 1,3-dipolar cycloaddition, electrocyclic rearrangement, sigmatropic rearrangement, and double group transfer prototypes. Focal point analyses (FPA) extrapolating to the ab initio limit were executed via explicit quantum chemical computations with electron correlation treatments through CCSDT(Q) and correlation-consistent Gaussian basis sets up to aug'-cc-pV5Z. Optimized geometric structures and vibrational frequencies of all stationary points were obtained at the CCSD(T)/cc-pVTZ level of theory. The FPA reaction barriers and energies exhibit convergence to within a few tenths of a kcal mol-1. The FPA benchmarks were used to evaluate the performance of 60 density functionals (eight dispersion-corrected), covering the local-density approximation (LDA), generalized gradient approximations (GGAs), meta-GGAs, hybrids, meta-hybrids, double-hybrids, and range-separated hybrids. The meta-hybrid M06-2X functional provided the best overall performance [mean absolute error (MAE) of 1.1 kcal mol-1] followed closely by the double-hybrids B2K-PLYP, mPW2K-PLYP, and revDSD-PBEP86 [MAE of 1.4-1.5 kcal mol-1]. The regularly used GGA functional BP86 gave a higher MAE of 5.8 kcal mol-1, but it qualitatively described the trends in reaction barriers and energies. Importantly, we established that accurate yet efficient meta-hybrid or double-hybrid DFT potential energy surfaces can be acquired based on geometries from the computationally efficient and robust BP86/DZP level.

Quantification of the Helicality of Helical Molecular Orbitals

The frontier molecular orbital (MO) topology of linear carbon molecules, such as polyynes, can be visually identified as helices. However, there is no clear way to quantify the helical curvature of these π-MOs, and it is thus challenging to quantify correlations between the helical curvature and molecular properties. In this paper, we develop a method that enables us to compute the helical curvature of MOs based on their nodal planes. Using this method, we define a robust way of quantifying the helical nature of MOs (helicality) by their deviation from a perfect helix. We explore several limiting cases, including polyynes, metallacumulenes, cyclic allenes, and spiroconjugated systems, where the change in helical curvature is subtle yet clearly highlighted with this method. For example, we show that strain only has a minor effect on the helicality of the frontier orbitals of cycloallenes and that the MOs of spiroconjugated systems are close to perfect helices around the spiro-carbon. Our work provides a well-defined method for assessing orbital helicality beyond visual inspection of MO isosurfaces, thus paving the way for future studies of how the helicality of π-MOs affects molecular properties.

Zinc Iodide Catalyzed Synthesis of Trisubstituted Allenes from Terminal Alkynes and Ketones

A straightforward, user-friendly, efficient protocol for the one pot, ZnI₂-catalyzed allenylation of terminal alkynes with pyrrolidine and ketones, toward trisubstituted allenes, is described. Trisubstituted allenes can be obtained under either conventional heating or microwave irradiation conditions, which significantly reduces the reaction time. A sustainable, widely available, and low-cost metal salt catalyst is employed, and the reactions are carried out under solvent-free conditions. Among others, synthetically valuable allenes bearing functionalities such as amide, hydroxyl, or phthalimide can be efficiently prepared. Mechanistic experiments, including kinetic isotope effect measurements and density functional theory (DFT) calculations, suggest a rate-determining [1,5]-hydride transfer during the transformation of the intermediate propargylamine to the final allene.

Switch From Pauli-Lowering to LUMO-Lowering Catalysis in Brønsted Acid-Catalyzed Aza-Diels-Alder Reactions

Brønsted acid-catalyzed inverse-electron demand (IED) aza-Diels-Alder reactions between 2-aza-dienes and ethylene were studied using quantum chemical calculations. The computed activation energy systematically decreases as the basic sites of the diene progressively become protonated. Our activation strain and Kohn-Sham molecular orbital analyses traced the origin of this enhanced reactivity to i) "Pauli-lowering catalysis" for mono-protonated 2-aza-dienes due to the induction of an asynchronous, but still concerted, reaction pathway that reduces the Pauli repulsion between the reactants; and ii) "LUMO-lowering catalysis" for multi-protonated 2-aza-dienes due to their highly stabilized LUMO(s) and more concerted synchronous reaction path that facilitates more efficient orbital overlaps in IED interactions. In all, we illustrate how the novel concept of "Pauli-lowering catalysis" can be overruled by the traditional concept of "LUMO-lowering catalysis" when the degree of LUMO stabilization is extreme as in the case of multi-protonated 2-aza-dienes.

Gold Catalysts Can Generate Nitrone Intermediates from a Nitrosoarene/Alkene Mixture, Enabling Two Distinct Catalytic Reactions: A Nitroso-Activated Cycloheptatriene/Benzylidene Rearrangement

Gold-catalyzed reactions of cycloheptatrienes with nitrosoarenes yield nitrone derivatives efficiently. This reaction sequence enables us to develop gold-catalyzed aerobic oxidations of cycloheptatrienes to afford benzaldehyde derivatives using CuCl and nitrosoarenes as co-catalysts (10-30 mol %). Our density functional theory calculations support a novel nitroso-activated rearrangement, tropylium → benzylidene. With the same nitrosoarenes, we developed their gold-catalyzed [2 + 2 + 1]-annulations between nitrosobenzene and two enol ethers to yield 5-alkoxyisoxazolidines using 1,4-cyclohexadienes as hydrogen donors.

Origins of Endo Selectivity in Diels-Alder Reactions of Cyclic Allene Dienophiles

Strained cyclic allenes, first discovered in 1966 by Wittig and co-workers, have recently emerged as valuable synthetic building blocks. Previous experimental investigations, and computations reported here, demonstrate that the Diels-Alder reactions of furans and pyrroles with 1,2-cyclohexadiene and oxa- and azaheterocyclic analogs proceed with endo selectivity. This endo selectivity gives the adduct with the allylic saturated carbon of the cyclic allene endo to the diene carbons. The selectivity is very general and useful in synthetic applications. Our computational study establishes the origins of this endo selectivity. We analyze the helical frontier molecular orbitals of strained cyclic allenes and show how secondary orbital and electrostatic effects influence stereoselectivity. The LUMO of carbon-3 of the allene (C-3 is not involved in primary orbital interactions) interacts in a stabilizing fashion with the HOMO of the diene in such a way that the carbon of the cyclic allene attached to C-1 favors the endo position in the transition state. The furan LUMO, allene HOMO interaction reinforces this preference. These mechanistic studies are expected to prompt the further use of long-avoided strained cyclic allenes in chemical synthesis.

Chemical reactivity from an activation strain perspective

Chemical reactions are ubiquitous in the universe, they are at the core of life, and they are essential for industrial processes. The drive for a deep understanding of how something occurs, in this case, the mechanism of a chemical reaction and the factors controlling its reactivity, is intrinsically valuable and an innate quality of humans. The level of insight and degree of understanding afforded by computational chemistry cannot be understated. The activation strain model is one of the most powerful tools in our arsenal to obtain unparalleled insight into reactivity. The relative energy of interacting reactants is evaluated along a reaction energy profile and related to the rigidity of the reactants' molecular structure and the strength of the stabilizing interactions between the deformed reactants: ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). Owing to the connectedness between the activation strain model and Kohn-Sham molecular orbital theory, one is able to obtain a causal relationship between both the sterics and electronics of the reactants and their mutual reactivity. Only when this is accomplished one can eclipse the phenomenological explanations that are commonplace in the literature and textbooks and begin to rationally tune and optimize chemical transformations. We showcase how the activation strain model is the ideal tool to elucidate fundamental organic reactions, the activation of small molecules by metallylenes, and the cycloaddition reactivity of cyclic diene- and dipolarophiles.

How Oriented External Electric Fields Modulate Reactivity

A judiciously oriented external electric field (OEEF) can catalyze a wide range of reactions and can even induce endo/exo stereoselectivity of cycloaddition reactions. The Diels-Alder reaction between cyclopentadiene and maleic anhydride is studied by using quantitative activation strain and Kohn-Sham molecular orbital theory to pinpoint the origin of these catalytic and stereoselective effects. Our quantitative model reveals that an OEEF along the reaction axis induces an enhanced electrostatic and orbital interaction between the reactants, which in turn lowers the reaction barrier. The stronger electrostatic interaction originates from an increased electron density difference between the reactants at the reactive center, and the enhanced orbital interaction arises from the promoted normal electron demand donor-acceptor interaction driven by the OEEF. An OEEF perpendicular to the plane of the reaction axis solely stabilizes the exo pathway of this reaction, whereas the endo pathway remains unaltered and efficiently steers the endo/exo stereoselectivity. The influence of the OEEF on the inverse electron demand Diels-Alder reaction is also investigated; unexpectedly, it inhibits the reaction, as the electric field now suppresses the critical inverse electron demand donor-acceptor interaction.

How the Lewis Base F- Catalyzes the 1,3-Dipolar Cycloaddition between Carbon Dioxide and Nitrilimines

The mechanism of the Lewis base F- catalyzed 1,3-dipolar cycloaddition between CO2 and nitrilimines is interrogated using DFT calculations. F- activates the nitrilimine, not CO2 as proposed in the literature, and imparts a significant rate enhancement for the cycloaddition. The origin of this catalysis is in the strength of the primary orbital interactions between the reactants. The Lewis base activated nitrilimine-F- has high-lying filled FMOs. The smaller FMO-LUMO gap promotes a rapid nucleophilic attack and overall cycloaddition with CO2.

Hetero-Diels–Alder reactions of 2H-phospholes with allenes: synthesis and functionalization of 6-methylene-1-phosphanorbornenes

The phospha-Diels–Alder reaction between 2H-phospholes and arylallenes affords 6-methylene-1-phosphanorbornenes in high yields with excellent regioselectivity. Further functionalization provides a 1-phosphanorbornene modified PCH₂CH₂P skeleton.