Conceptual, Qualitative, and Quantitative Theories of 1,3-Dipolar and Diels–Alder Cycloadditions Used in Synthesis

Combined activation strain model and energy decomposition analysis methods: a new way to understand pericyclic reactions

The recently introduced activation strain model (ASM) has allowed us to gain more insight into the intimacies of different fundamental processes in chemistry. In combination with the energy decomposition analysis (EDA) method, we have nowadays a very useful tool to quantitatively understand the physical factors that govern the activation barriers of reactions within organic and organometallic chemistry. In this Perspective article, we present selected illustrative examples of the application of this method to pericyclic reactions (Diels-Alder and double group transfer reactions) to show that this methodology nicely complements other more traditional, widely used theoretical methods.

Understanding the domino reaction between 3-chloroindoles and methyl coumalate yielding carbazoles. A DFT study

The molecular mechanism of the reaction between N-methyl-3-chloroindole and methyl coumalate yielding carbazole has been studied using DFT methods at the MPWB1K/6-311G(d,p) level in toluene. This reaction is a domino process that comprises three consecutive reactions: (i) a polar Diels-Alder (P-DA) reaction between indole and methyl coumalate yielding two stereoisomeric [2 + 4] cycloadducts (CAs); (ii) the elimination of HCl from these CAs affording two stereoisomeric intermediates; and (iii) the extrusion of CO2 in these intermediates, finally yielding the carbazole. This P-DA reaction proceeds in a completely regioselective and slightly exo selective fashion. In spite of the highly polar character of this P-DA reaction, it presents a high activation enthalpy of 21.8 kcal mol(-1) due to the loss of the aromatic character of the indole during the C-C bond formation. Thermodynamic calculations suggest that the P-DA reaction is the rate-determining step of this domino reaction; in addition, the initial HCl elimination in the formal [2 + 4] CAs is kinetically favoured over the extrusion of CO2. Although the P-DA reaction is kinetically and thermodynamically very unfavourable, the easier HCl and CO2 elimination from the [2 + 4] CAs together with the strong exergonic character of the CO2 extrusion makes the P-DA reaction irreversible. An ELF topological analysis of the bonding changes along the P-DA reaction supports a two-stage one-step mechanism. An analysis of the global DFT reactivity indices at the ground state of the reagents confirms the highly polar character of this P-DA reaction. Finally, the complete regioselectivity of the studied reactions can be explained using the Parr functions.

Diazo groups endure metabolism and enable chemoselectivity in cellulo

We introduce a stabilized diazo group as a reporter for chemical biology. ManDiaz, which is a diazo derivative of N-acetylmannosamine, is found to endure cellular metabolism and label the surface of a mammalian cell. There its diazo group can undergo a 1,3-dipolar cycloaddition with a strained alkyne, providing a signal comparable to that from the azido congener, ManNAz. The chemoselectivity of diazo and alkynyl groups enables dual labeling of cells that is not possible with azido and alkynyl groups. Thus, the diazo group, which is approximately half the size of an azido group, provides unique opportunities for orthogonal labeling of cellular components.

Mechanism of [3+2] cycloaddition of alkynes to the [Mo3 S4 (acac)3 (py)3 ][PF6 ] cluster

A study, involving kinetic measurements on the stopped-flow and conventional UV/Vis timescales, ESI-MS, NMR spectroscopy and DFT calculations, has been carried out to understand the mechanism of the reaction of [Mo3 S4 (acac)3 (py)3 ][PF6 ] ([1]PF6 ; acac=acetylacetonate, py=pyridine) with two RCCR alkynes (R=CH2 OH (btd), COOH (adc)) in CH3 CN. Both reactions show polyphasic kinetics, but experimental and computational data indicate that alkyne activation occurs in a single kinetic step through a concerted mechanism similar to that of organic [3+2] cycloaddition reactions, in this case through the interaction with one Mo(μ-S)2 moiety of [1](+) . The rate of this step is three orders of magnitude faster for adc than that for btd, and the products initially formed evolve in subsequent steps into compounds that result from substitution of py ligands or from reorganization to give species with different structures. Activation strain analysis of the [3+2] cycloaddition step reveals that the deformation of the two reactants has a small contribution to the difference in the computed activation barriers, which is mainly associated with the change in the extent of their interaction at the transition-state structures. Subsequent frontier molecular orbital analysis shows that the carboxylic acid substituents on adc stabilize its HOMO and LUMO orbitals with respect to those on btd due to better electron-withdrawing properties. As a result, the frontier molecular orbitals of the cluster and alkyne become closer in energy; this allows a stronger interaction.

A bonding evolution theory study of the mechanism of [3+2] cycloaddition reactions of nitrones with electron-deficient ethylenes

BET study of the mechanism of zw-type [3+2] cycloaddition reactions of nitrones with electron-deficient ethylenes.

A DFT study of the role of the Lewis acid catalysts in the [3 + 2] cycloaddition reaction of the electrophilic nitrone isomer of methyl glyoxylate oxime with nucleophilic cyclopentene

The mechanism and stereoselectivity of the BH₃-catalysed 32CA reaction between C-methoxycarbonyl nitrone and cyclopentene has been studied using MPWB1K/6-31G(d) computational level.

Non-classical CH⋯O hydrogen-bond determining the regio- and stereoselectivity in the [3 + 2] cycloaddition reaction of (Z)-C-phenyl-N-methylnitrone with dimethyl 2-benzylidenecyclopropane-1,1-dicarboxylate. A topological electron-density study

Formation of a non-classical CH⋯O hydrogen-bond involving the nitrone C–H hydrogen is responsible for the selectivity experimentally found in this non-polar zw-type 32CA reaction.

Understanding the high reactivity of carbonyl compounds towards nucleophilic carbenoid intermediates generated from carbene isocyanides

The high nucleophilic character of the carbenoid intermediate cis-IN together with the specific approach mode of acetone make the formation of the C–C single bond with a very low activation free energy, possible.

Distortion–interaction analysis along the reaction pathway to reveal the reactivity of the Alder-ene reaction of enes

The reactivity of uncatalyzed Alder-ene type reactions of hetero-substituted propylene is interpreted by distortion–interaction analysis of both the transition states and the complete reaction pathways.

In silico study on the mechanism of formation of hydrazine and nitrogen in the reactions of excess hydroxylamine with 2,4-dinitrophenyl diethyl phosphate

Decomposition study of 2,4-dinitrophenyl diethyl phosphate to hydrazine and nitrogen gas with excess of hydroxylamine using quantum chemical calculations.

Theoretical study of the BINOL–zinc complex-catalyzed asymmetric inverse-electron-demand imino Diels–Alder reaction: mechanism and stereochemistry

The enantioselectivity originates from the hindrance of a BINOL ligand, and the exo-selectivity is achieved by the favored electrophilic/nucleophilic interaction.

The origin of regio- and stereoselectivity in the 1,3-dipolar cycloaddition of nitrile oxides with C1-substituted 7-oxabenzonorbornadienes, a DFT study

The origin ofexo/antiselectivity in the 1,3-dipolar cycloaddition of nitrile oxides with C₁-substituted 7-oxabenzonorbornadienes has been investigated theoretically.

A review of syntheses of 1,5-disubstituted tetrazole derivatives

This report provides a brief overview of the various representative literature procedures for the synthesis of 1,5-disubstituted tetrazoles (1,5-DSTs) and fused 1,5-disubstituted tetrazoles with more than 120 references. Most of the published methods for the synthesis of 1,5-DSTs include the use of nitriles, amides, thioamides, imidoyl chlorides, heterocumulenes, isocyanates, isothiocyanates, carbodiimides, ketenimines, ketones, amines, and alkenes as the starting materials. The transformation of 1- and 5-substituted tetrazoles into 1,5-DSTs is also covered in this report.

Diels-Alder reactions of chiral isoimidium salts: a computational study

Recently, important efforts have been devoted to asymmetric Diels-Alder (DA) cycloadditions. Several chiral auxiliaries and catalysts were tested, originating a multitude of selectivities. Here, we study the ability of the isoimidium group as a dienophile activator in DA reactions, as well as its behavior in the induction of selectivity, when incorporated in chiral auxiliary units. We study dienophiles attached to isoimidium auxiliaries derived from (2R,5R)-2,5-diphenylpyrrolidine and from (R)-bis((R)-1-phenylethyl)amine, and show that they lead to low activation energies in DA additions to different dienes. Reported experimental regio- and endo/exo selectitivites are also fully rationalized. While diastereoselectivities originated by (2R,5R)-2,5-diphenylpyrrolidine based dienophiles can easily be rationalized by a C2 symmetric transition state, several transition states have to be simultaneously accounted for the rationalization of the selectivity obtained with dienophiles based on (R)-bis((R)-1-phenylethyl)amine. In this case, the C2 symmetric structure leads to opposite selectivities to those experimentally observed. Thus, while the structures of the dienophiles derived from these two amines seem similar, their behavior in the induction of stereoselectivity in DA reactions is quite different. Our models, which substantially differ from those previously proposed in the literature, can also be adapted to other reactions in which this type of chiral auxiliaries is used.

Origin of Reactivity Trends of Noble Gas Endohedral Fullerenes Ng2@C60 (Ng = He to Xe)

We have computationally studied the factors governing the enhanced Diels-Alder reactivity of noble gas endohedral fullerenes Ng2@C60 when Ng = Ar, Kr, and Xe as compared to Ng = none, He, and Ne. To this end, we have employed the activation strain model of reactivity in combination with the energy decomposition analysis (EDA) method in DFT calculations on the Diels-Alder cycloaddition reaction between Ng2@C60 and 1,3-butadiene. Our results indicate that when heavier noble gas dimers are introduced inside the C60 cage, dramatic effects on both the geometrical and electronic structure of the fullerenic cage occur leading to a remarkable enhanced interaction between the deformed reactants along the entire reaction coordinate.

A quantum chemical topological analysis of the C-C bond formation in organic reactions involving cationic species

ELF topological analysis of the ionic Diels-Alder (I-DA) reaction between the N,N-dimethyliminium cation and cyclopentadiene (Cp) has been performed in order to characterise the C-C single bond formation. The C-C bond formation begins in the short range of 2.00-1.96 Åvia a C-to-C pseudoradical coupling between the most electrophilic center of the iminium cation and one of the two most nucleophilic centers of Cp. The electron density of the pseudoradical center generated at the most electrophilic carbon of the iminium cation comes mainly from the global charge transfer which takes place along the reaction. Analysis of the global reactivity indices indicates that the very high electrophilic character of the iminium cation is responsible for the negative activation energy found in the gas phase. On the other hand, the analysis of the radical P(k)(o) Parr functions of the iminium cation, and the nucleophilic P(k)(-) Parr functions of Cp makes the characterisation of the most favourable two-center interaction along the formation of the C-C single bond possible.

The activation strain model and molecular orbital theory: understanding and designing chemical reactions

In this Tutorial Review, we make the point that a true understanding of trends in reactivity (as opposed to measuring or simply computing them) requires a causal reactivity model. To this end, we present and discuss the Activation Strain Model (ASM). The ASM establishes the desired causal relationship between reaction barriers, on one hand, and the properties of reactants and characteristics of reaction mechanisms, on the other hand. In the ASM, the potential energy surface ΔE(ζ) along the reaction coordinate ζ is decomposed into the strain ΔEstrain(ζ) of the reactants that become increasingly deformed as the reaction proceeds, plus the interaction ΔEint(ζ) between these deformed reactants, i.e., ΔE(ζ) = ΔEstrain(ζ) + ΔEint(ζ). The ASM can be used in conjunction with any quantum chemical program. An analysis of the method and its application to problems in organic and organometallic chemistry illustrate the power of the ASM as a unifying concept and a tool for rational design of reactants and catalysts.

The mechanism of ionic Diels–Alder reactions. A DFT study of the oxa-Povarov reaction

Topological ELF analysis along these I-DA reactions indicates that both mechanisms present a similar C–C bond formation.

A new C–C bond formation model based on the quantum chemical topology of electron density

Pseudodiradical structures and GEDT involved in the C–C single bond formation in non-polar, polar and ionic organic reactions.

Theoretical study on the molecular mechanism of the [5 + 2] vs. [4 + 2] cyclization mediated by Lewis acid in the quinone system

The thermal and Lewis acid (LA) catalyzed cyclizations of quinone 1 involved in the synthesis of Colombiasin A and Elipsaterosin B have been theoretically studied using DFT methods at the B3LYP/6-311G(d,p) computational level. B3LYP calculations suggest that the formal endo [4 + 2] cycloadduct allowing the synthesis of Colombiasin A is preferentially formed under thermal conditions, while in the presence of the BF3 LA catalyst the formal [5 + 2] cycloadduct is seen, allowing the synthesis of Elipsaterosin B. The BF3 LA catalyst not only accelerates the nucleophilic attack on the C2 carbon of the quinone framework through a more polar C-C bond formation, but also provokes a different electron density rearrangement along the nucleophilic attack favoring the subsequent C-C bond formation at the C4 carbon with the formation of the formal [5 + 2] cycloadduct. ELF bonding analysis along these cyclizations indicates that the C-C single bond formation takes place in the range of 1.91-2.1 Å by C-to-C coupling of two pseudoradical centers. Along the formation of the first C2-C9 single bond, these pseudoradical centers appear at one of the most electrophilic and at one of the most nucleophilic centers of quinone 1, C2 and C9 carbons, respectively. Analysis of the Parr functions suggests that although the most favorable electrophilic/nucleophilic interaction is that involving the C2 carbon of quinone and the C12 carbon of the butadiene framework, the intramolecular nature of the cyclization prevents the corresponding reactive channel.