Computational Methods To Calculate Accurate Activation and Reaction Energies of 1,3-Dipolar Cycloadditions of 24 1,3-Dipoles

Periselectivity and ambimodal transition states in cycloadditions of tetrachloro-o-benzoquinone with 6,6-dimethylfulvene

The reaction mechanism of cycloadditions of tetrachloro-o-benzoquinone with 6,6-dimethylfulvene were systematically investigated with density functional theory calculations. It was found that conditional primary interactions stabilize the ambimodal transition states in the endo pathways. Ambimodal transition states lead to [6 + 4]/[4 + 2] adducts or [4 + 2]/[2 + 4] adducts, which interconvert through 3,3-sigmatropic shift reactions. The substituent effects on periselectivity were also investigated.

Kinetics of N2 Release from Diazo Compounds: A Combined Machine Learning-Density Functional Theory Study

Diazo compounds are commonly employed as carbene precursors in carbene transfer reactions during a variety of functionalization procedures. Release of N2 gas from diazo compounds may lead to carbene formation, and the ease of this process is highly dependent on the characteristics of the substituents located in the vicinity of the diazo moiety. A quantum mechanical density functional theory assisted by machine learning was used to investigate the relationship between the chemical features of diazo compounds and the activation energy required for N2 elimination. Our results suggest that diazo molecules, possessing a higher positive partial charge on the carbene carbon and more negative charge on the terminal nitrogen, encounter a lower energy barrier. A more positive C charge decreases the π-donor ability of the carbene lone pair to the π* orbital of N2, while the more negative N charge is a result of a weak interaction between N2 lone pair and vacant p orbital of the carbene. The findings of this study can pave the way for molecular engineering for the purpose of carbene generation, which serves as a crucial intermediate for many chemical transformations in synthetic chemistry.

Computational Study on Radical-Mediated Thiol-Epoxy Reactions

Radical-mediated thiol-epoxy reactions were elucidated for analyzing the overlap problem of the thiol-ene/thiol-epoxy systems using computational approaches. Nine epoxy model molecules were evaluated to mimic the chemical structures and reactivity of some industrial epoxy molecules. Modeling reaction mechanisms was conducted through density functional theory (DFT) calculations using the M06-2X/6-31+G(d,p) level at 1.0 atm and 298.15 K. An analog thiol-ene mechanism was proposed for radical-mediated thiol-epoxide reactions. Unlike the thiol-ene reactions, the addition reaction to epoxides is relatively slow (rate constants <10-4 M-1 s-1). However, the chain transfer, which paves the way for the overlapping of dual curing systems, is quite fast (rate constants >101 M-1 s-1). High stability of thiyl radicals, epoxy ring strain, and the instability of formed alkoxy radical from addition reaction were emphasized as the main driving forces for the reaction energetics and kinetics. Control of temperature and using certain thiols are strongly recommended to avoid curing step overlap based on the findings in this study.

Orthogonal Inverse-Electron-Demand Cycloaddition Reactions Controlled by Frontier Molecular Orbital Interactions

Chemoselective pairs of bioorthogonal reactants enable the simultaneous labeling of several biomolecules. Here, we access orthogonal click reactions by exploiting differences in frontier molecular orbital interaction energies in transition states. We establish that five-membered cyclic dienes are inert to isonitriles but readily react with strained alkynes, while tetrazines with bulky substituents readily react with isonitriles. Strained alkynes show an opposite reactivity pattern. The approach was demonstrated by orthogonally labeling two proteins with different fluorophores.

Substituent Effects in Bioorthogonal Diels-Alder Reactions of 1,2,4,5-Tetrazines

1,2,4,5-Tetrazines are increasingly used as reactants in bioorthogonal chemistry due to their high reactivity in Diels-Alder reactions with various dienophiles. Substituents in the 3- and 6-positions of the tetrazine scaffold are known to have a significant impact on the rate of cycloadditions; this is commonly explained on the basis of frontier molecular orbital theory. In contrast, we show that reactivity differences between commonly used classes of tetrazines are not controlled by frontier molecular orbital interactions. In particular, we demonstrate that mono-substituted tetrazines show high reactivity due to decreased Pauli repulsion, which leads to a more asynchronous approach associated with reduced distortion energy. This follows the recent Vermeeren-Hamlin-Bickelhaupt model of reactivity increase in asymmetric Diels-Alder reactions. In addition, we reveal that ethylene is not a good model compound for other alkenes in Diels-Alder reactions.

One-Bond-Nucleophilicity and -Electrophilicity Parameters: An Efficient Ordering System for 1,3-Dipolar Cycloadditions

Diazoalkanes are ambiphilic 1,3-dipoles that undergo fast Huisgen cycloadditions with both electron-rich and electron-poor dipolarophiles but react slowly with alkenes of low polarity. Frontier molecular orbital (FMO) theory considering the 3-center-4-electron π-system of the propargyl fragment of diazoalkanes is commonly applied to rationalize these reactivity trends. However, we recently found that a change in the mechanism from cycloadditions to azo couplings takes place due to the existence of a previously overlooked lower-lying unoccupied molecular orbital. We now propose an alternative approach to analyze 1,3-dipolar cycloaddition reactions, which relies on the linear free energy relationship lg k₂(20 °C) = s_N(N + E) (eq 1) with two solvent-dependent parameters (N, s_N) to characterize nucleophiles and one parameter (E) for electrophiles. Rate constants for the cycloadditions of diazoalkanes with dipolarophiles were measured and compared with those calculated for the formation of zwitterions by eq 1. The difference between experimental and predicted Gibbs energies of activation is interpreted as the energy of concert, i.e., the stabilization of the transition states by the concerted formation of two new bonds. By linking the plot of lg k₂ vs N for nucleophilic dipolarophiles with that of lg k₂ vs E for electrophilic dipolarophiles, one obtains V-shaped plots which provide absolute rate constants for the stepwise reactions on the borderlines. These plots furthermore predict relative reactivities of dipolarophiles in concerted, highly asynchronous cycloadditions more precisely than the classical correlations of rate constants with FMO energies or ionization potentials. DFT calculations using the SMD solvent model confirm these interpretations.

Regioselective synthesis of enantiopure 1,2- and 1,3-dispirooxindoles along with a DFT study

In the present study, a library of important enantiopure dispirooxindole [indolizidine, pyrrolizidine, and pyrrolidine] derivatives with three or four contiguous and two quaternary stereogenic centers using different amino acids (pipecolic acid, sarcosine, proline and hydroxyproline) were synthesized in high yields (up to 96%) through a regio- and diastereoselective (up to 99 : 1) multicomponent 1,3-dipolar cycloaddition strategy. Based on the results, the alteration of amino acids led to a change in the regioselectivity and unusual regioisomers (pyrrolizidine versus indolizidine/pyrrolidine) were obtained to construct a novel enantiopure 1,3-dispirooxindole skeleton. The stereochemical outcome of the cycloaddition was determined by single crystal X-ray diffraction analysis and the self-disproportionation of enantiomers (SDE) test confirmed the enantiomeric purity of the desired products. The mechanism and differences in the regioselectivity of the 1,3-dipolar cycloaddition reactions between the stable azomethane ylides obtained from ninhydrin, pipecolinic acid, and proline with (E)-2-oxoindolin-3-ylideneacetyl sultam were theoretically studied through DFT calculations at the M06-2X/6-31G(d,p) level in methanol.

Fluoro, Trifluoromethyl, and Trifluoroacetyl Substituent Effects on Cycloaddition Reactivities: Computations and Analysis

The importance of fluoro and trifluoromethyl substituents in drug effectiveness prompted the computational exploration of fluorine-containing substituents in valuable synthetic cycloadditions. Diels-Alder or 1,3-dipolar cycloaddition reactions of typical reactants, cyclopentadiene, N-phenyldiazoacetamide, tetrazine, and N-phenylsydnone involving fluorine-containing substituents (F, CF₃, and COCF₃) were studied with M06-2X density functional theory. Inductive and conjugative effects influence normal and inverse electron-demand reactions differently. These results provide a guide to the design and use of cycloadditions for the introduction of fluoro and trifluoromethyl substituents in synthetic processes.

Photoinduced Oxygen Transfer Using Nitroarenes for the Anaerobic Cleavage of Alkenes

Herein we report the anaerobic cleavage of alkenes into carbonyl compounds using nitroarenes as oxygen transfer reagents under visible light. This approach serves as a safe and practical alternative to mainstream oxidative cleavage protocols, such as ozonolysis and the Lemieux-Johnson reaction. A wide range of alkenes possessing oxidatively sensitive functionalities underwent anaerobic cleavage to generate carbonyl derivatives with high efficiency and regioselectivity. Mechanistic studies support that the transformation occurs via direct photoexcitation of the nitroarene followed by a nonstereospecific radical cycloaddition event with alkenes. This leads to 1,3,2- and 1,4,2-dioxazolidine intermediates that fragment to give the carbonyl products. A combination of radical clock experiments and in situ photoNMR spectroscopy revealed the identities of the key radical species and the putative aryl dioxazolidine intermediates, respectively.

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.

A Theoretical Evaluation of the Behavior of Nitrosoamidine upon Reacting with Methoxy Butadiene, as Potential Heterodiene or Heterodienophile

Abstract:

The molecular mechanism of experimentally observed regio- and chemoselectivity of the cycloaddition reaction of nitrosoamidine 1 and 1-methoxy butadiene 2 has been investigated using DFT calculations at M06-2X/cc-pVDZ level. Accordingly, the possible reaction pathways and factors, which govern selectivity are investigated systematically. Analysis of the calculated results show that the most favorable cyclization reaction takes place through the [2+4] endo-proximal pathway, which is under kinetically and thermodynamically controls. Moreover, analysis of the global and local reactivity indices correctly explains the source of the experimentally observed regio- and chemoselectivity. The electron localization function (ELF) analysis of some selected points along the IRC profile of the most preferred pathway suggests that the reaction takes place via a two-stage one-step mechanism. NCI topological analysis of the possible pathways of [2+4] cycloaddition reaction of 1-E and 2-Z reveals the roles of the attractive interactions between reaction sites, the weak noncovalent interactions in the endo approaches, and the repulsive interactions in the regio- and stereoselectivity of the reaction.

Multi-Ion Bridged Pathway of N-Oxides to 1,3-Dipole Dilithium Oxide Complexes

Roussi's landmark work on the generation of 1,3-dipoles from tertiary amine N-oxides has not reached its full potential since its underlying mechanism is neither well explored nor understood. Two competing mechanisms were previously proposed to explain the transformation involving either an iminium ion or a diradical intermediate. Our investigation has revealed an alternative mechanistic pathway that explains experimental results and provides significant insights to guide the creation of new N-oxide reagents beyond tertiary alkylamines for direct synthetic transformations. Truhlar's M06-2x functional and Møller-Plesset second-order perturbation theory with Dunning's [jul,aug]-cc-pv[D,T]z basis sets and discrete-continuum solvation models were employed to determine activation enthalpies and structures. During these mechanistic explorations, we discovered a unique multi-ion bridged pathway resulting from the rate-determining step, which was energetically more favorable than other alternate mechanisms. This newly proposed mechanism contains no electrophilic intermediates, strengthening the reaction potential by broadening the reagent scope and limiting the possible side reactions. This thoroughly defined general mechanism supports a more direct route for improving the use of N-oxides in generating azomethine ylide-dilithium oxide complexes with expanded functional group tolerance and breadth of chemistry.

Comparison of (5 + 2) Cycloadditions Involving Oxidopyrylium and Oxidopyridinium Ions: Relative Reactivities

A variety of (5 + 2) cycloaddition reactions involving oxidopyridinium and oxidopyrylium zwitterions are compared to investigate the effects of nitrogen-for-oxygen substitution on reactivity. Activation barriers for nitrogen-containing systems are predicted to be larger than those for analogous oxygen-containing systems. Correlations between barrier heights and synchronicity of C-C bond formation, changes to aromaticity, reactant distortion, and interaction energies between zwitterions and alkenes were assessed, leading to the conclusion that reactivity depends more on distortion effects (including aromaticity loss) than on interaction effects (such as those associated with highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) interactions).

Theoretical insight on the treatment of β-hexachlorocyclohexane waste through alkaline dehydrochlorination

The occurrence of 4.8-7.2 million tons of hexachlorocyclohexane (HCH) isomers stocked in dumpsites around the world constitutes a huge environmental and economical challenge because of their toxicity and persistence. Alkaline treatment of an HCH mixture in a dehydrochlorination reaction is hampered by the low reactivity of the β-HCH isomer (HCl elimination unavoidably occurring through syn H-C-C-Cl arrangements). More intriguingly, the preferential formation of 1,2,4-trichlorobenzene in the β-HCH dehydrochlorination reaction (despite the larger thermodynamical stability of the 1,3,5-isomer) has remained unexplained up to now, though several kinetic studies had been reported. In this paper, we firstly show a detailed Density Functional study on all paths for the hydroxide anion-induced elimination of β-HCH through a three-stage reaction mechanism (involving two types of reaction intermediates). We have now demonstrated that the first reaction intermediate can follow several alternative paths, the preferred route involving abstraction of the most acidic allylic hydrogen which leads to a second reaction intermediate yielding only 1,2,4-trichlorobenzene as the final reaction product. Our theoretical results allow explaining the available experimental data on the β-HCH dehydrochlorination reaction (rate-determining step, regioselectivity, instability of some reaction intermediates).

Electrophilic reactivities of cyclic enones and α,β-unsaturated lactones

The reactivities of cyclic enones and α,β-unsaturated lactones were characterized by following the kinetics of their reactions with colored carbon-centered reference nucleophiles in DMSO at 20 °C. The experimentally determined second-order rate constants k₂ were analyzed with the Mayr–Patz equation, lg k = s_N(N + E), to furnish the electrophilicity descriptors E for the Michael acceptors. Cyclic enones and lactones show different reactivity trends than their acyclic analogs. While cyclization reduces the reactivity of enones slightly, α,β-unsaturated lactones are significantly more reactive Michael acceptors than analogously substituted open-chain esters. The observed reactivity trends were rationalized through quantum-chemically calculated Gibbs energy profiles (at the SMD(DMSO)/M06-2X/6-31+G(d,p) level of theory) and distortion interaction analysis for the reactions of the cyclic Michael acceptors with a sulfonium ylide. The electrophilicities of simplified electrophilic fragments reflect the general reactivity pattern of structurally more complex terpene-derived cyclic enones and sesquiterpene lactones, such as parthenolide.

Different reactivity trends for cyclic and acyclic Michael acceptors were found within the framework of Mayr's experimental reactivity scales and analyzed through quantum-chemical studies.

1,3-Dipolar Cycloadditions by a Unified Perspective Based on Conceptual and Thermodynamics Models of Chemical Reactivity

The main aim in the present report is to gain a deeper understanding of typical 1,3-dipolar cycloadditions by means of three chemical reactivity models in a unified perspective: conceptual density functional theory, distortion/interaction, and reaction force analysis. The focus is to explore the information provided by each reactivity model and how they complement or reinforce each other. Our results showed that the Bell-Evans-Polanyi (BEP) relationship is fulfilled, which is consistent with the Hammond-Leffler postulate. The electronic chemical potential based analysis classifies the reactions as HOMO-, HOMO/LUMO-, and LUMO-controlled reactions as the activation energy increases. It seems likely that HOMO-controlled reaction shifts into LUMO-controlled one as the transition state (TS) position does from early into late. Therefore, the transition from HOMO- (and early TS) into LUMO-controlled (and late TS) is paid by shifting the overall energy change into an endothermic direction, thus supporting the fulfillment of the BEP principle. While thermodynamic models unveil that the distortion or structural rearrangements mainly drive the activation barriers rather than interaction or electronic rearrangements in accord with the distortion/interaction and reaction force analysis, respectively. It is also found that both models are consistent when energy associated with structural and electronic reordering from reaction force analysis is respectively confronted with destabilizing (distortion and Pauli repulsion) and stabilizing (electrostatic and orbital interactions) contributions from the distortion/interaction model, which, on the other hand, increases as low activation barrier and high exothermicity are converted into the high barrier and low exothermicity along with the BEP relation. Finally, the reaction force constant reveals that all 1,3-dipolar cycloaddition reactions proceed by a synchronous single-step mechanism, unveiling that the degree of synchronicity is quite the same in all reactions, confirming the statement that BEP is fulfilled for similar reactions proceeding by a quite alike degree of synchronicity.

The simplest Diels-Alder reactions are not endo-selective

There is a widespread perception that the high level of endo selectivity witnessed in many Diels-Alder reactions is an intrinsic feature of the transformation. In contrast to expectations based upon this existing belief, the first experimental Diels-Alder reactions of a novel, deuterium-labeled 1,3-butadiene with commonly used mono-substituted alkenic dienophiles (acrolein, methyl vinyl ketone, acrylic acid, methyl acrylate, acrylamide and acrylonitrile) reveal kinetic endo : exo ratios close to 1 : 1. Maleonitrile, butenolide, α-methylene γ-butyrolactone, and N-methylmaleimide behave differently, as does methyl vinyl ketone under Lewis acid catalysis. CBS-QB3 calculations incorporating solvent and temperature parameters give endo : exo product ratios that are in near quantitative agreement with these and earlier experimental findings. This work challenges the preconception of innate endo-selectivity by providing the first experimental evidence that the simplest Diels-Alder reactions are not endo-selective. Trends in behaviour are traced to steric and electronic effects in Diels-Alder transition structures, giving new insights into these fundamental processes.

Quantitative Dynamics of the N2O + C2H2 → Oxadiazole Reaction: A Model for 1,3-Dipolar Cycloadditions

The reaction N₂O + C₂H₂ → oxadiazole has been considered as a prototype for 1,3-dipolar cycloadditions. Here, we report a comprehensive dynamical study of this important reaction on a full-dimensional potential energy surface, which is fitted to about 64 000 high-level ab initio data by a machine learning approach. Comprehensive dynamical simulations are carried out to provide quantitative chemical insight into its reaction dynamics. In addition to confirming the enhancement effect of the N₂O bending mode on the reactivity, intricate mode specificity effects of other vibrational modes in reactants are revealed for the first time. The asymmetric stretching mode of N₂O and the C-C-H bending mode of C₂H₂ show no effect. All remaining modes can enhance the reactivity. In particular, the vibrational excitation of the N₂O symmetric stretching mode shows similar enhancement effect on the title reaction, compared to its bending mode excitation. Detailed analysis reveals that the concerted mechanism dominates with the reactants propelled sufficiently close to each other to yield product. This study advances our understanding of the chemical dynamics of the title reaction.

Ring-opening carbonyl-olefin metathesis of norbornenes

A computational and experimental study of the hydrazine-catalyzed ring-opening carbonyl-olefin metathesis of norbornenes is described. Detailed theoretical investigation of the energetic landscape for the full reaction pathway with six different hydrazines revealed several crucial aspects for the design of next-generation hydrazine catalysts. This study indicated that a [2.2.2]-bicyclic hydrazine should offer substantially increased reactivity versus the previously reported [2.2.1]-hydrazine due to a lowered activation barrier for the rate-determining cycloreversion step, a prediction which was verified experimentally. Optimized conditions for both cycloaddition and cycloreversion steps were identified, and a brief substrate scope study for each was conducted. A complication for catalysis was found to be the slow hydrolysis of the ring-opened hydrazonium intermediates, which were shown to suffer from a competitive and irreversible cycloaddition with a second equivalent of norbornene. This problem was overcome by the strategic incorporation of a bridgehead methyl group on the norbornene ring, leading to the first demonstrated catalytic carbonyl-olefin metathesis of norbornene rings.

Synthetic Entry to Polyfunctionalized Molecules through the [3+2]-Cycloaddition of Thiocarbonyl Ylides

Here we present a comprehensive study on the [3+2]-cycloaddition of thiocarbonyl ylides with a wide variety of alkenes and alkynes. The obtained dihydro- and tetrahydrothiophene products serve as exceptionally versatile intermediates providing access to thiophenes, dienes, dendralenes, and vic-quarternary carbon centers. The use of high-pressure conditions enables thermally unstable, sterically encumbered or moderately reactive substrates to undergo the cycloaddition under mild conditions, thereby increasing the yield by up to 58%. In addition, we showcase its utility by the formal syntheses of the pharmaceuticals NGB 4420 and tenilapine.

Fluorodibenzocyclooctynes: A Trackable Click Reagent with Enhanced Reactivity

Bioorthogonal reactions have widespread applications in biological systems, and development of new bioorthogonal reactions has been of great interest over the past two decades. In this work, the design and synthesis of a family of fluorinated dibenzocyclooctynes (FDIBOs) are reported. The electron-deficient nature of fluorine atoms significantly accelerated the reaction of cyclooctynes in 1,3-dipolar cycloadditions, with either benzyl azide or ethyl diazoacetate, compared to conventional dibenzocyclooctyne (DIBO). In addition, FDIBOs showed unique trackable properties owing to the high NMR sensitivity of the naturally abundant ¹⁹ F isotope. Biological molecules, including a monosaccharide, a peptide, and a protein, were tested with FDIBOs, and these reactions could be easily monitored by ¹⁹ F NMR spectroscopy to evaluate the progress of the conjugation reactions. In addition, labeling of live cells was also demonstrated with metabolically modified bacteria to expand the possible applications of FDIBOs.

Role of Water in the Reaction Mechanism and endo/exo Selectivity of 1,3-Dipolar Cycloadditions Elucidated by Quantum Chemistry and Machine Learning

Asymmetric 1,3-dipolar cycloadditions of azomethine ylides with activated olefins are among the most important and versatile methods for the synthesis of enantioenriched pyrroline and pyrrolidine derivatives. Despite both theoretical and practical importance, the role of water molecules in the reactivity and endo/exo selectivity remains unclear. To explore how water accelerates the reactions and improves the endo/exo selectivity of the cycloadditions of 1,3-dipole phthalazinium-2-dicyanomethanide (1) and two dipolarophiles, an ab initio-quality neural network potential that overcomes the computational bottleneck of explicitly considering water molecules was used. It is demonstrated that not only the nature of both the dipolarophile and the 1,3-dipole, but also the solvent medium, can perturb or even alter the reaction mechanism. An extreme case was found for the reaction of 1,3-dipole 1 with methyl vinyl ketone, in which the reaction mechanism changes from a concerted to a stepwise mode on going from MeCN to H₂ O as solvent, with formation of a zwitterionic intermediate that is a very shallow minimum on the energy surface. Thus, high stereocontrol can still be expected despite the stepwise nature of the mechanism. The results indicate that water can induce global polarization along the reaction coordinate and highlight the role of microsolvation effects and bulk-phase effects in reproducing the experimentally observed aqueous acceleration and enhanced endo/exo selectivity.

Understanding the mechanism of the 1,3-dipolar cycloaddition reaction between a thioformaldehyde S-oxide and cyclobutadiene: Competition between the stepwise and concerted routes

Changing the mechanism of the widely used 1,3-dipolar cycloaddition reaction from its usual asynchronous one-step pattern to the rarely observed stepwise form leads to the emergence of intermediates, side products, and other impurities. Thus, it is crucial to determine the nature of the mechanism of the 1,3-dipolar cycloaddition reaction between a special 1,3-dipole and a specified dipolarophile (by theoretical methods) before using them for synthesizing a desired product. In this study, therefore, we have investigated the possibility of some probable intermediates emergence in the 1,3-dipolar cycloaddition reaction between cyclobutadiene and thioformaldehyde S-oxide. The results showed that emergence of Int (B) (−52.1 kcal mol−1) via transition state (B-1) is favorable both thermodynamically and kinetically (in comparison with all other stepwise routes). That is, developing probable impurities should not be neglected at least in the cases of the reactions between some thioformaldehyde S-oxide and some dipolarophiles.

Structural Distortion of Cycloalkynes Influences Cycloaddition Rates both by Strain and Interaction Energies

The reactivities of 2‐butyne, cycloheptyne, cyclooctyne, and cyclononyne in the 1,3‐dipolar cycloaddition reaction with methyl azide were evaluated through DFT calculations at the M06‐2X/6‐311++G(d)//M06‐2X/6‐31+G(d) level of theory. Computed activation free energies for the cycloadditions of cycloalkynes are 16.5–22.0 kcal mol⁻¹ lower in energy than that of the acyclic 2‐butyne. The strained or predistorted nature of cycloalkynes is often solely used to rationalize this significant rate enhancement. Our distortion/interaction–activation strain analysis has been revealed that the degree of geometrical predistortion of the cycloalkyne ground‐state geometries acts to enhance reactivity compared with that of acyclic alkynes through three distinct mechanisms, not only due to (i) a reduced strain or distortion energy, but also to (ii) a smaller HOMO–LUMO gap, and (iii) an enhanced orbital overlap, which both contribute to more stabilizing orbital interactions.

Benchmark study of popular density functionals for calculating binding energies of three-center two-electron bonds

Density functional theory (DFT) can be used to study the three-center two-electron (3c2e) bonding mode, which is universal in catalysts containing alkaline-earth (Ae) and boron-group (Bg) elements. However, because of the delocalization pattern of the 3c2e bond, the wavefunction cannot be accurately described by DFT methods. The calculated energies of Ae and Bg catalysts therefore fluctuate greatly when different functionals are used, largely because of inconsistent DFT-calculated binding energies of 3c2e bonds. Nevertheless, with the development of supercomputers and theoretical calculation software, the DFT method is becoming increasingly popular for studying Ae and Bg catalysts. In this study, we compared the performances of 21 functionals with the high-level composite G3B3 method in calculations for the binding energies of 3c2e bonds. Several frequently used post-Hartree-Fock methods were also tested. The calculation results indicate that the M06-2X, MN12-L, and MN15 functionals give consistent and reliable binding energies for common 3c2e bonds. © 2018 Wiley Periodicals, Inc.

Identification of the Criegee intermediate reaction network in ethylene ozonolysis: impact on energy conversion strategies and atmospheric chemistry

The reaction network of the simplest Criegee intermediate (CI) CH₂OO has been studied experimentally during the ozonolysis of ethylene.

Effect of the exchange–correlation functional on the synchronicity/nonsynchronicity in bond formation in Diels–Alder reactions: a reaction force constant analysis

The performance of 24 KS-DFT-based methods (GGA, MGGA, HGGA, HMGGA, and DHGGA) was assessed, finding that M11 and M06-2X (HMGGA) predicting reliable TS geometries, energetics, and (a)synchronicities in Diels–Alder reactions.

Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution

Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowest-energy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.

Hyperconjugative Aromaticity and Antiaromaticity Control the Reactivities and π-Facial Stereoselectivities of 5-Substituted Cyclopentadiene Diels-Alder Cycloadditions

The reactivities and π-facial stereoselectivities of Diels-Alder reactions of 5-substituted cyclopentadienes were studied using density functional theory. Burnell and co-workers previously showed that the π-facial selectivities result from the energies required to distort the reactants into the transition state geometries. We have discovered the origins of these distortions. C₅-X σ-donors predistort the cyclopentadiene into an envelope conformation that maximizes the stabilizing hyperconjugative interaction between the C₅-X σ-bond and the diene π-system. This envelope conformation geometrically resembles the anti transition state. To minimize the destabilizing effect of negative hyperconjugation, C₅-X σ-acceptors predistort in the opposite direction toward an envelope geometry that resembles the syn transition state. We now show how hyperconjugative effects of the C₅-X substituent influence the stereoselectivities and have developed a unified model rationalizing the stereoselectivities and reactivities of 5-substituted cyclopentadiene Diels-Alder reactions.

Biosynthesis of Grandione: An Example of Tandem Hetero Diels-Alder/Retro-Claisen Rearrangement Reaction?

Mechanistic theoretical studies about the feasibility of the traditional proposed mechanism of formation for icetexane diterpene dimer grandione were assessed using density functional method at the M06-2X/6-31G(d,p) level of theory. Bulk water solvent effects were taken into account implicitly using the polarizable continuum model (SCI-PCM). The results were compared with the selectivity found in the biomimetic synthesis performed by experimental research groups. The relative free energy calculation shows that the one-step H-DA formation mechanism nominated in the literature is not a viable mechanism. We found that an alternative competing Tandem pathway is consistent with the experimental trends. Thus, our results suggested that the compound grandione is formed via a H-DA/retro-Claisen rearrangement and not by the traditional H-DA mechanism proposed early in the experimental studies. The H-DA initial step produce a biecyclic adduct followed by a domino retro-Claisen rearrangement that releases the energy strain of the bicyclic intermediary. Steric issues and hyperconjugation interactions are the mainly factors driving the reaction nature and the selectivity in the formation reaction. Finally, the enzymatic assistance for dimer formation was analyzed in terms of the calculated transition state energy barrier.

Origins of halogen effects in bioorthogonal sydnone cycloadditions

Halogen substituents increase sydnone cycloaddition reactivities substantially. Fluoro-sydnones are superior to bromo- and chloro-sydnones, and can achieve extremely high second-order rate constants with strained alkynes. Computational studies have revealed the fluorine substituent increases the reactivity of sydnone mainly by lowering its distortion energy.

A computational model to predict the Diels-Alder reactivity of aryl/alkyl-substituted tetrazines

Abstract

The tetrazine ligation is one of the fastest bioorthogonal ligations and plays a pivotal role in time-critical in vitro and in vivo applications. However, prediction of the reactivity of tetrazines in inverse electron demand Diels–Alder-initiated ligation reactions is not straight-forward. Commonly used tools such as frontier molecular orbital theory only give qualitative and often even wrong results. Applying density functional theory, we have been able to develop a simple computational method for the prediction of the reactivity of aryl/alkyl-substituted tetrazines in inverse electron demand Diels–Alder reactions.

Graphical Abstract

Electronic supplementary material

The online version of this article (10.1007/s00706-017-2110-x) contains supplementary material, which is available to authorized users.

Organocopper triggered cyclization of conjugated dienynes via tandem SN2′/Alder-ene reaction

Propargylic carbonates were converted to indenes through a S_N2′/Alder-ene cascade triggered by organocopper reagents.

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.