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

Antileishmanial activity of new hybrid tetrahydroquinoline and quinoline derivatives with phosphorus substituents

Heterocyclic compounds, such as hybrid tetrahydroquinoline and quinoline derivatives with phosphorated groups, have been prepared by multicomponent cycloaddition reaction between phosphorus-substituted anilines, aldehydes and styrenes. The antileishmanial activity of these compounds has been evaluated on both promastigotes and intramacrophagic amastigotes of Leishmania infantum. Good antileishmanial activity of functionalized tetrahydroquinolines 4a, 5a, 6b and quinoline 8b has been observed with similar activity than the standard drug amphotericin B and close selective index (SI between 43 and 57) towards L. infantum amastigotes to amphotericin B. Special interest shows tetrahydroquinolylphosphine sulfide 5a with an EC₅₀ value (0.61 ± 0.18 μM) similar to the standard drug amphotericin B (0.32 ± 0.05 μM) and selective index (SI = 56.87). In addition, compound 4c shows remarkable inhibition on Leishmania topoisomerase IB. Parallel theoretical study of stereoelectronic properties, application of docking-based virtual screening methods, along with molecular electrostatic potential and predictive druggability analyses are also reported.

Terminal Alkenes from Acrylic Acid Derivatives via Non-Oxidative Enzymatic Decarboxylation by Ferulic Acid Decarboxylases

Fungal ferulic acid decarboxylases (FDCs) belong to the UbiD-family of enzymes and catalyse the reversible (de)carboxylation of cinnamic acid derivatives through the use of a prenylated flavin cofactor. The latter is synthesised by the flavin prenyltransferase UbiX. Herein, we demonstrate the applicability of FDC/UbiX expressing cells for both isolated enzyme and whole-cell biocatalysis. FDCs exhibit high activity with total turnover numbers (TTN) of up to 55000 and turnover frequency (TOF) of up to 370 min-1. Co-solvent compatibility studies revealed FDC's tolerance to some organic solvents up 20 % v/v. Using the in-vitro (de)carboxylase activity of holo-FDC as well as whole-cell biocatalysts, we performed a substrate profiling study of three FDCs, providing insights into structural determinants of activity. FDCs display broad substrate tolerance towards a wide range of acrylic acid derivatives bearing (hetero)cyclic or olefinic substituents at C3 affording conversions of up to >99 %. The synthetic utility of FDCs was demonstrated by a preparative-scale decarboxylation.

DFT exploration of [3 + 2] cycloaddition reaction of 1H-phosphorinium-3-olate and 1-methylphosphorinium-3-olate with methyl methacrylate

A Molecular Electron Density Theory (MEDT) study of the regio- and stereoselectivity of the [3 + 2] cycloaddition (32CA) reaction of 1H-phosphorinium-3-olate and 1-methylphosphorinium-3-olate with methyl methacrylate was carried out using the B3LYP/6-31G(d) method. In order to test the method dependence for the most favorable reaction path leading to the 1H-substituted 6-exo cycloadduct (CA) various functionals using higher basis sets were taken into consideration in the gas phase. An analysis of the energetic parameters indicates that the reaction path leading to 6-exo CA are kinetically as well as thermodynamically favored in the gas phase, THF and ethanol. The calculated energetic parameters of the 32CA reaction of these phosphorus derivatives were compared with those of methyl acrylate and their nitrogen analogues. Investigation of the global electron density transfer at the TSs indicates that these 32CA reactions have non-polar character, while electron localisation function topological analysis of the C-C bond formation along the most favorable reaction path indicates that these 32CA reactions take place through a non-concerted two-stage one-step mechanism, via highly asynchronous TSs.

Electronic Structure Analysis of the Diels-Alder Cycloaddition Catalyzed by Alkali-Exchanged Faujasites

The Diels-Alder cycloaddition (DAC) reaction is a commonly employed reaction for the formation of C-C bonds. DAC catalysis can be achieved by using Lewis acids and via reactant confinement in aqueous nanocages. Low-silica alkali-exchanged faujasite catalysts combine these two factors in one material. They can be used in the tandem DAC/dehydration reaction of biomass-derived 2,5-dimethylfuran (DMF) with ethylene toward p-xylene, in which the DAC reaction step initiates the overall reaction cycle. In this work, we performed periodic density functional theory (DFT) calculations on the DAC reaction between DMF and C2H4 in low-silica alkali(M)-exchanged faujasites (MY; Si/Al = 2.4; M = Li+, Na+, K+, Rb+, Cs+). The aim was to investigate how confinement of reactants in MY catalysts changed their electronic structure and the DAC-reactivity trend among the evaluated MY zeolites. The conventional high-silica alkali-exchanged isolated site model (MFAU; Si/Al = 47) served as a reference. The results show that confinement leads to initial-state (IS) destabilization and transition-state (TS) stabilization. Among the tested MY, most significant IS destabilization is found in RbY. Only antibonding orbital interactions between the reactants/reactive complex and cations were found, indicating that TS stabilization arises from ionic interactions. Additionally, in RbY the geometry of the transition state is geometrically most similar to that of the initial and final state. RbY also exhibits an optimal combination of the confinement-effects, resulting in having the lowest computed DAC-activation energy. The overall effect is a DAC-reactivity trend inversion in MY as compared to the trend found in MFAU where the activation energy correlates with the Lewis acidity of the exchangeable cations.

Substituted 1,5-naphthyridine derivatives as novel antileishmanial agents. Synthesis and biological evaluation

Visceral leishmaniasis is a parasitic disease that affects, among other areas, both sides of the Mediterranean Basin. The drugs classically used in clinical practice are pentavalent antimonials (Sb^V) and amphotericin B, which are nephrotoxic, require parenteral administration, and increasing drug resistance in visceral leishmaniasis has been observed. These circumstances justify the search of new families of compounds to find effective drugs against the disease. Eukaryotic type I DNA topoisomerase (TopIB) has been found essential for the viability of the parasites, and therefore represents a promising target in the development of an antileishmanial therapy. In this search, heterocyclic compounds, such as 1,5-naphthyridines, have been prepared by cycloaddition reaction between N-(3-pyridyl)aldimines and acetylenes and their antileishmanial activity on promastigotes and amastigote-infected splenocytes of Leishmania infantum has been evaluated. In addition, the cytotoxic effects of newly synthesized compounds were assessed on host murine splenocytes in order to calculate the corresponding selective indexes (SI). Excellent antileishmanial activity of 1,5-naphthyridine 19, 21, 22, 24 and 27 has been observed with similar activity than the standard drug amphotericin B and higher selective index (SI > 100) towards L. infantum amastigotes than amphotericin B (SI > 62.5). Special interest shows the 1,5-naphthyridine 22 with an IC₅₀ value (0.58 ± 0.03 μM) similar to the standard drug amphotericin B (0.32 ± 0.05 μM) and with the highest selective index (SI = 271.5). In addition, this compound shows remarkable inhibition on leishmanial TopIB. However, despite these interesting results, further studies are needed to disclose other potential targets involved in the antileishmanial effect of these novel compounds.

1,4-Additions of tricyclic 1,4-diphosphinines - a novel system to study σ-bond activation and π-π dispersion interactions

The dienic nature of the aromatic π-system in 1,4-diphosphinines remains largely unexplored to this day due to a lack of facile and efficient synthetic protocols. Recently reported stable, tricyclic 1,4-diphosphinines were used to explore the thermal reactivity of the π-system towards an array of dienophiles in [4π+2π]- and, for the first time, in [4π+2σ]-type cycloaddition reactions.

Bioorthogonal Cycloadditions: Computational Analysis with the Distortion/Interaction Model and Predictions of Reactivities

Bioorthogonal chemistry has had a major impact on the study of biological processes in vivo. Biomolecules of interest can be tracked by using probes and reporters that do not react with cellular components and do not interfere with metabolic processes in living cells. Much time and effort has been devoted to the screening of potential bioorthogonal reagents experimentally. This Account describes how our groups have performed computational screening of reactivity and mutual orthogonality. Our collaborations with experimentalists have led to the development of new and useful reactions. Dozens of bioorthogonal cycloadditions have been reported in the literature in the past few years, but as interest in tracking multiple targets arises, our computational screening has gained importance for the discovery of new mutually orthogonal bioorthogonal cycloaddition pairs. The reactivities of strained alkenes and alkynes with common 1,3-dipoles such as azides, along with mesoionic sydnones and other novel 1,3-dipoles, have been explored. Studies of "inverse-electron-demand" dienes such as triazines and tetrazines that have been used in bioorthogonal Diels-Alder cycloadditions are described. The color graphics we have developed give a snapshot of whether reactions are fast enough for cellular applications (green), adequately reactive for labeling (yellow), or only useful for synthesis or do not occur at all (red). The colors of each box give an instant view of rates, while bar graphs provide an analysis of the factors that control reactivity. This analysis uses the distortion/interaction or activation strain model of cycloaddition reactivity developed independently by our group and that of F. Matthias Bickelhaupt in The Netherlands. The model analyzes activation barriers in terms of the energy required to distort the reactants to the transition state geometry. This energy, called the distortion energy or activation strain, constitutes the major component of the activation energy. The strong bonding interaction between the termini of the two reactants, which we call the interaction energy, overcomes the distortion energy and leads to the new bonds in the products. This Account describes how we have analyzed and predicted bioorthogonal cycloaddition reactivity using the distortion/interaction model and how our experimental collaborators have employed these insights to create new bioorthogonal cycloadditions. The graphics we use document and predict which combinations of cycloadditions will be useful in bioorthogonal chemistry and which pairs of reactions are mutually orthogonal. For example, the fast reaction of 5-phenyl-1,2,4-triazine and a thiacycloheptyne will not interfere with the other fast reaction of 3,6-diphenyl-1,2,4,5-tetrazine and a cyclopropene. No cross reactions will occur, as these are very slow reactions.

Prediction of the Regioselectivity of 1,3-Dipolar Cycloaddition Reactions of Nitrile Oxides with 2(5H)-Furanones Using Recent Theoretical Reactivity Indices

The regioselectivity of a series of 16 1,3-dipolar cycloaddition reactions of nitrile oxides with 2(5 H)-furanones has been analysed by means of global and local electrophilic and nucleophilic reactivity indices using density functional theory at the B3LYP level together with the 6-31G(d) basis set. The local electrophilicity and nucleophilicity indices, based on Fukui and Parr functions, have been calculated for the terminal sites, namely the C1 and O3 atoms of the 1,3-dipole and the C4 and C5 atoms of the dipolarophile. These local indices were calculated using both Mulliken and natural charges and spin densities. The results obtained show that the C5 atom of the 2(5 H)-furanones is the most electrophilic site whereas the O3 atom of the nitrile oxides is the most nucleophilic centre. It turns out that the experimental regioselectivity is correctly reproduced, indicating that both Fukui- and Parr-based indices are efficient tools for the prediction of the regiochemistry of the studied reactions and could be used for the prediction of new designed reactions of the same kind.

From Mechanistic Study to Chiral Catalyst Optimization: Theoretical Insight into Binaphthophosphepine-catalyzed Asymmetric Intramolecular [3 + 2] Cycloaddition

Density functional M11 was used to study the mechanism and enantioselectivity of a binaphthophosphepine-catalyzed intramolecular [3 + 2] cycloaddition reaction. The computational results revealed that this reaction proceeds through nucleophilic addition of the phosphine catalyst to the allene, which yields a zwitterionic phosphonium intermediate. The subsequent stepwise [3 + 2] annulation process, which starts with the intramolecular nucleophilic addition of the allenoate moiety to the electron-deficient olefin group, determines the enantioselectivity of the reaction. This step is followed by a ring-closing reaction and water-assisted proton-transfer process to afford the final product with concomitant regeneration of the phosphine catalyst. Theoretical predictions of the enantioselectivity for various phosphine catalysts were consistent with experimental observations, and 2D contour maps played an important role in explaining the origin of the enantioselectivity. Moreover, on the basis of our theoretical study, new binaphthophosphepine catalysts were designed and that are expecting to afford higher enantioselectivity in this cycloaddition reaction.

Study of the Hetero-[4+2]-Cycloaddition Reaction of Aldimines and Alkynes. Synthesis of 1,5-Naphthyridine and Isoindolone Derivatives

Both experimental and computational studies for the cycloaddition reaction between N-(3-pyridyl)aldimines and acetylenes where 1,5-naphthyridines are obtained are reported. The reaction of benzaldimine with a methoxycarbonyl group in position 2 with phenyl acetylene, styrene, and indene afforded polycyclic isoindolone derivatives. The mechanism of reaction of N-(3-pyridyl)aldimines with olefins can be explained by an asynchronous [4+2] cycloaddition; in the case of acetylenes, the obtained results suggest a stepwise mechanism through a 3-azatriene.

Fine-Tuning Strain and Electronic Activation of Strain-Promoted 1,3-Dipolar Cycloadditions with Endocyclic Sulfamates in SNO-OCTs

The ability to achieve predictable control over the polarization of strained cycloalkynes can influence their behavior in subsequent reactions, providing opportunities to increase both rate and chemoselectivity. A series of new heterocyclic strained cyclooctynes containing a sulfamate backbone (SNO-OCTs) were prepared under mild conditions by employing ring expansions of silylated methyleneaziridines. SNO-OCT derivative 8 outpaced even a difluorinated cyclooctyne in a 1,3-dipolar cycloaddition with benzylazide. The various orbital interactions of the propargylic and homopropargylic heteroatoms in SNO-OCT were explored both experimentally and computationally. The inclusion of these heteroatoms had a positive impact on stability and reactivity, where electronic effects could be utilized to relieve ring strain. The choice of the heteroatom combinations in various SNO-OCTs significantly affected the alkyne geometries, thus illustrating a new strategy for modulating strain via remote substituents. Additionally, this unique heteroatom activation was capable of accelerating the rate of reaction of SNO-OCT with diazoacetamide over azidoacetamide, opening the possibility of further method development in the context of chemoselective, bioorthogonal labeling.

New mechanistic interpretations for nitrone reactivity

The reactivity of nitrones in cycloadditions and related reactions is revisited by introducing a topological perspective.

Regio- and stereoselective synthesis of novel isoxazolidine heterocycles by 1,3-dipolar cycloaddition between C-phenyl-N-methylnitrone and substituted alkenes. Experimental and DFT investigation of selectivity and mechanism

A series of isoxazolidine heterocycles was synthesized through the 1,3-dipolar cycloaddition (13DC) reaction of C-phenyl-N-methylnitrone with different substituted alkenes.

1,3-Dipolar Cycloaddition with Diazo Groups: Noncovalent Interactions Overwhelm Strain

Like azides, diazoacetamides undergo 1,3-dipolar cycloadditions with oxanorbornadienes (OND) in a reaction that is accelerated by the relief of strain in the transition state. The cycloaddition of a diazoacetamide with unstrained ethyl 4,4,4-trifluoro-2-butynoate is, however, 35-fold faster than with the analogous OND because of favorable interactions with the fluoro groups. Its rate constant (k = 0.53 M(-1) s(-1) in methanol) is comparable to those of strain-promoted azide-cyclooctyne cycloadditions.

Decreasing Distortion Energies without Strain: Diazo-Selective 1,3-Dipolar Cycloadditions

The diazo group has attributes that complement those of the azido group for applications in chemical biology. Here, we use computational analyses to provide insights into the chemoselectivity of the diazo group in 1,3-dipolar cycloadditions. Dipole distortion energies are responsible for ∼80% of the overall energetic barrier for these reactions. Here, we show that diazo compounds, unlike azides, provide an opportunity to decrease that barrier substantially without introducing strain into the dipolarophile. The ensuing rate enhancement is due to the greater nucleophilic character of a diazo group compared to that of an azido group, which can accommodate decreased distortion energies without predistortion. The tuning of distortion energies with substituents in a diazo compound or dipolarophile can enhance reactivity and selectivity in a predictable manner. Notably, these advantages of diazo groups are amplified in water. Our findings provide a theoretical framework that can guide the design and application of both diazo compounds and azides in "orthogonal" contexts, especially for biological investigations.

DFT study on the regio- and stereo-selectivity of the Diels–Alder reaction between a cycloprop-2-ene carboxylate and some cyclic 1,3-dienes

A study of the reactivity and regio- and stereo-selectivity of Diels-Alder reactions of 2-methyl-3-propionylcycloprop-2-ene carboxylic acid methyl ester with cyclohexa-1,3-diene derivatives and furan, in the gas phase, has been carried out using density functional theory (DFT)-based reactivity indices and activation energies. Four reaction channels associated with ortho (or meta), meta (or para), endo and exo pathways have been explored and characterised. The activation energies indicate that the endo pathways are preferred and DFT-based reactivity indices clearly predict the stereochemistry of the isolated cycloadducts.

1,3-Dipolar Cycloadditions of Diazo Compounds in the Presence of Azides

The diazo group has untapped utility in chemical biology. The tolerance of stabilized diazo groups to cellular metabolism is comparable to that of azido groups. However, chemoselectivity has been elusive, as both groups undergo 1,3-dipolar cycloadditions with strained alkynes. Removing strain and tuning dipolarophile electronics yields diazo group selective 1,3-dipolar cycloadditions that can be performed in the presence of an azido group. For example, diazoacetamide but not its azido congener react with dehydroalanine residues, as in the natural product nisin.

Cycloaddition Reactions of Indanedioneketene with Electron-Rich Dienophiles: An Experimental and a Theoretical Study

Thermal decomposition of the phenyliodonium ylide of lawsone gives rise to a highly reactive cyclic α,α'-dioxoketene, indanedioneketene, which reacts with electron-rich dienophiles such as enol ethers to afford [4 + 2] cycloadducts. The initially formed 2,3-dihydro-2-alkoxy-indeno[1,2-b]pyrano-4,5-diones are labile compounds since through an opening of the pyranone ring upon heating they easily tautomerize to alkoxyallylidene-indenedione derivatives and under acid-catalysis they are additionally transformed to 2-(1,3-dihydroxyallylidene)-1H-indene-1,3(2H)-dione or by loss of alcohol to indeno[1,2-b]pyran-4,5-diones. A DFT study explains the polar nature of the cycloaddition reaction, the observed reactivity and suggests a possible mechanism operating in these reactions.

Asymmetric Syntheses of the Flavonoid Diels-Alder Natural Products Sanggenons C and O

Metal-catalyzed, double Claisen rearrangement of a bis-allyloxyflavone has been utilized to enable a concise synthesis of the hydrobenzofuro[3,2-b]chromenone core structure of the natural products sanggenon A and sanggenol F. In addition, catalytic, enantioselective [4+2] cycloadditions of 2'-hydroxychalcones have been accomplished using B(OPh)3/BINOL complexes. Asymmetric syntheses of the flavonoid Diels-Alder natural products sanggenons C and O have been achieved employing a stereodivergent reaction of a racemic mixture (stereodivergent RRM) involving [4+2] cycloaddition.

On the mechanism of retro-Diels–Alder reaction of partially saturated 2-pyrones to produce biorenewable chemicals

Partially saturated 2-pyrone molecules undergo ring-opening and decarboxylation via retro-Diels–Alder (rDA) reaction.

Understanding the stereoselectivity in Brønsted acid catalysed Povarov reactions generating cis/trans CF3-substituted tetrahydroquinolines: a DFT study

Stereochemistry in the Brønsted acid catalysed Povarov reactions.

Theoretical study of the regio- and stereoselectivity of the intramolecular Povarov reactions yielding 5H-chromeno[2,3-c] acridine derivatives

The intramolecular Povarov (IMP) reactions involved in the synthesis of 5H-chromeno[2,3-c] acridine derivatives [Tetrahedron Lett., 2010, 51, 3071–3074] have been studied using density functional theory (DFT) methods.

A theoretical study on the hetero-Diels–Alder reaction of phosphorous substituted diaza- and oxaza-alkenes with olefins derivatives

DFT studies indicated that a hetero-Diels–Alder reaction of 4-phosphinyl and 4-phosphonyl-1,2-diaza- and 1,2-oxaza-1,3-butadienes with some olefins take place via an asynchronous concerted mechanism through endo or exo transition states.