Origins of the Unfavorable Activation and Reaction Energies of 1-Azadiene Heterocycles Compared to 2-Azadiene Heterocycles in Diels–Alder Reactions

Unveiling the Reaction Mechanism of Diels-Alder Cycloadditions between 2,5-Dimethylfuran and Ethylene Derivatives Using Topological Tools

The [4+2] Diels-Alder cycloaddition reaction between 2,5-DMF (1) and ethylene derivatives (2 a-h) activated by electron-withdrawing groups has been studied at the density functional theory level using a panoply of tools to unravel the reaction mechanisms. From the analysis of the reactivity indices, 2 a-h behave as electrophiles while 1 as nucleophile, and the activation of the double bond of ethylene increases its electrophilicity, which is accompanied by an enhancement of the polarity of the reaction. The activation Gibbs free energy decreases linearly as a function of this increase of polarity, as estimated by the electrophilicity difference between the reactants. The difference of electrophilicity drives also the global electron density transfer at the transition state and the asynchronicity of the reaction, as evaluated by the difference of carbon-carbon bond lengths in the transition state. Then, Bonding Evolution Theory shows that the activation of the double bond of ethylene by an electron-withdrawing group changes the reaction mechanism from a one-step synchronous process to a one-step asynchronous process. Generally, the endo pathway is kinetically favored but, thermodynamically, it is the exo pathway. Finally, using the Distortion/Interaction-Activation Strain, it is shown that the endo/exo selectivity is mostly driven by the differences of interaction energies.

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.

Modular approach to non-aromatic and aromatic pyrroles through gold-catalyzed [3 + 2] cycloaddition of 2H-azirines and ynamides

The developed modular approach to hard-to-reach non-aromatic 3H- and 2H-pyrroles is based on the integration of 2H-azirines and ynamides.

Click Chemistry with Cyclopentadiene

Cyclopentadiene is one of the most reactive dienes in normal electron-demand Diels-Alder reactions. The high reactivities and yields of cyclopentadiene cycloadditions make them ideal as click reactions. In this review, we discuss the history of the cyclopentadiene cycloaddition as well as applications of cyclopentadiene click reactions. Our emphasis is on experimental and theoretical studies on the reactivity and stability of cyclopentadiene and cyclopentadiene derivatives.

Understanding chemical reactivity using the activation strain model

Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms-that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system.

Maleimide-based metal-free ligation with dienes: a comparative study

Maleimide-based Diels–Alder strategies for bioconjugation are compared in terms of dienes accessibility and stability, reactions rates, as well as products isolation and stability.

PyFrag 2019-Automating the exploration and analysis of reaction mechanisms

We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Theoretical study on reaction mechanism of synthesis of iridium complexes having cyclometalated acyclic diaminocarbene ancillary ligands

DFT calculations at the M06-2X level were performed to explore the reaction mechanism for the synthesis of the new cyclometalated iridium(III) complexes with acyclic diaminocarbene ancillary ligands. The solvent effects of the reaction systems have been considered by a single-point energy calculation using the SMD model in the experimental conditions of CH₂Cl₂ solvent. The calculated results show that the reaction consists of two main steps: the first step is the hydrogen transfer between the two N atoms, and the next step is the closed-loop process of the Ir atom and the aromatic ring ortho to release the HCl molecule. The reaction has a relatively low activation free energy of 17.1-23.2 kcal mol^-1, indicating that it is easy to occur under the experimental conditions of Na et al. At the same time, it was found that the aryl para-CF₃ substituent has higher reactivity than the corresponding reactant of the NO₂ substituent.

Factors Controlling the Diels-Alder Reactivity of Hetero-1,3-Butadienes

We have quantum chemically explored the Diels-Alder reactivities of a systematic series of hetero-1,3-butadienes with ethylene by using density functional theory at the BP86/TZ2P level. Activation strain analyses provided physical insight into the factors controlling the relative cycloaddition reactivity of aza- and oxa-1,3-butadienes. We find that dienes with a terminal heteroatom, such as 2-propen-1-imine (NCCC) or acrolein (OCCC), are less reactive than the archetypal 1,3-butadiene (CCCC), primarily owing to weaker orbital interactions between the more electronegative heteroatoms with ethylene. Thus, the addition of a second heteroatom at the other terminal position (NCCN and OCCO) further reduces the reactivity. However, the introduction of a nitrogen atom in the backbone (CNCC) leads to enhanced reactivity, owing to less Pauli repulsion resulting from polarization of the diene HOMO in CNCC towards the nitrogen atom and away from the terminal carbon atom. The Diels-Alder reactions of ethenyl-diazene (NNCC) and 1,3-diaza-butadiene (NCNC), which contain heteroatoms at both the terminal and backbone positions, are much more reactive due to less activation strain compared to CCCC.

Probing the Structural and Electronic Effects on the Origin of π-Facial Stereoselectivity in 1-Methylphosphole 1-Oxide Cycloadditions and Cyclodimerization

We have examined the π-facial stereoselectivity in the Diels-Alder reactions of phosphole oxides computationally. The experimentally observed syn-cycloadditions have been rationalized with the Cieplak model and distortion-interaction model. The natural bond orbital analysis suggests that the hyperconjugative interactions are energetically preferred between the antiperiplanar methyl group present in the -P=O unit and the developing incipient (-C-C-) bond in syn-adducts in accordance with the Cieplak model. The distortion-interaction analysis carried out for syn and anti transition states of Diels-Alder reactions of 1-substituted phosphole 1-oxide with different dienophiles reveals that the syn selectivity is favored by distortions and interaction energies compared with the anti selectivity. The formation of a syn adduct is also stabilized by the π_CC-σ*_PO orbital interaction, and the repulsive n-π interaction destabilizes the anti adduct that leads to the 7.0 kcal/mol thermodynamic preference for the former adduct. Furthermore, the distortion-interaction model rationalizes the formation of stereospecific products in these Diels-Alder reactions, which however is not explicable with the much-debated Cieplak model.

Origin of π-Facial Stereoselectivity in Thiophene 1-Oxide Cycloadditions

We report a DFT computational study (M06-2X) of π-facial selectivity in the Diels-Alder reactions of thiophene 1-oxide. The preference for the syn cycloaddition arises because the ground state geometry of thiophene 1-oxide is predistorted into an envelope conformation that resembles the syn transition state geometry. The syn distortion occurs to minimize the effect of hyperconjugative antiaromaticity in the thiophene 1-oxide, arising from overlap of the σ*_SO with the π-system. The syn selectivity follows through to the product structure that is stabilized by a π-σ*_SO interaction, related to the 7-norbornenyl ion stability.

Confinement induced thermodynamic and kinetic facilitation of some Diels-Alder reactions inside a CB[7] cavitand

The effect of geometrical confinement on the Diels-Alder reactions between some model dienes viz. furan, thiophene, cyclopentadiene, benzene, and a classic dienophile, ethylene has been explored by performing density functional theory-based calculations. The effect of confinement has been imposed by a rigid macrocyclic molecule cucurbit[7]uril (CB[7]). Results indicate that all the reactions become thermodynamically more favorable at 298.15 K temperature and one atmospheric pressure inside CB[7] as compared to the corresponding free gaseous state reactions. Moreover, the rate constants associated with the reactions experience manifold enhancement inside CB[7] as compared to the "unconfined" reactions. Suitable contribution from the entropy factor makes the concerned reactions more facile inside CB[7]. The energy gap between the frontier molecular orbitals of the dienes and dienophiles decrease inside CB[7] as compared to that in the free state reactions thereby allowing facile orbital interactions. The nature of interaction as well as bonding has been analyzed with the help of atoms-in-molecules, noncovalent interaction, natural bond orbital as well as energy decomposition analyses. Results suggest that all the guests bind with CB[7] in an attractive fashion. Primarily, noncovalent interactions stabilize the host-guest systems. © 2017 Wiley Periodicals, Inc.

Influence of Endo- and Exocyclic Heteroatoms on Stabilities and 1,3-Dipolar Cycloaddition Reactivities of Mesoionic Azomethine Ylides and Imines

The geometries, stabilities, and 1,3-dipolar cycloaddition reactivities of 24 mesoionic azomethine ylides and imines were investigated using density functional theory calculations at the M06-2X/6-311+G-(d,p)/M06-2X/6-31G-(d) level. The computed structures highlight how the commonly used "aromatic" resonance form should be replaced by two more accurate resonance structures. Stabilities of the dipoles were assessed by various homodesmotic schemes and are consistent with these compounds being nonaromatic. The activation free energies with ethylene or acetylene range from 11.8 to 36.6 kcal/mol. Within each dipole type, the predicted cycloaddition reactivities correlate with the reaction energies and the resonance stabilization energies provided by the various substituents. Endocyclic (X) heteroatoms increase the reactivity of the 1,3-dipoles in the order of O > NH ≅ S, whereas exocyclic (Y) substituents increase it in the order of CH₂ > NH > O > S. Distortion/interaction analysis indicated that the difference in reactivity between differently substituted 1,3-dipoles is driven by distortion, whereas the difference between azomethine ylides and imines is related to lower interaction energies of imines with the dipolarophiles.

Synthesis of [18 F]Fluoroarenes by Nucleophilic Radiofluorination of N-Arylsydnones

A practical method for radiofluorination of anilines with [18 F]fluoride via N-arylsydnone intermediates is described. These precursors are stable, easy to handle and facilitate direct and regioselective 18 F-labeling to prepare [18 F]fluoroarenes. The value of this methodology is further highlighted by successful application to prepare an 18 F-labeled neuropeptide.

Theoretical Analysis of the Retro-Diels-Alder Reactivity of Oxanorbornadiene Thiol and Amine Adducts

Additions of amines or thiols to 7-oxanorbornadienes promote retro-[4 + 2] reactions to yield furans. Substitution at the bridgehead position also greatly influences the stability of the oxanorbornene adducts. Activation and reaction energies were computed with the M06-2X density functional, the origins of amine and thiol promoted fragmentation, and how substituent effects control fragmentation rates and reaction energetics are reported.