Cinchona-Based Hydrogen-Bond Donor Organocatalyst Metal Complexes: Asymmetric Catalysis and Structure Determination

In this study, we describe the synthesis of cinchona (thio)squaramide and a novel cinchona thiourea organocatalyst. These catalysts were employed in pharmaceutically relevant catalytic asymmetric reactions, such as Michael, Friedel-Crafts, and A3 coupling reactions, in combination with Ag(I), Cu(II), and Ni(II) salts. We identified several organocatalyst-metal salt combinations that led to a significant increase in both yield and enantioselectivity. To gain insight into the active catalyst species, we prepared organocatalyst-metal complexes and characterized them using HRMS, NMR spectroscopy, and quantum chemical calculations (B3LYP-D4/def2-TZVP), which allowed us to establish a structure-activity relationship.

A genetic optimization strategy with generality in asymmetric organocatalysis as a primary target

A catalyst possessing a broad substrate scope, in terms of both turnover and enantioselectivity, is sometimes called "general". Despite their great utility in asymmetric synthesis, truly general catalysts are difficult or expensive to discover via traditional high-throughput screening and are, therefore, rare. Existing computational tools accelerate the evaluation of reaction conditions from a pre-defined set of experiments to identify the most general ones, but cannot generate entirely new catalysts with enhanced substrate breadth. For these reasons, we report an inverse design strategy based on the open-source genetic algorithm NaviCatGA and on the OSCAR database of organocatalysts to simultaneously probe the catalyst and substrate scope and optimize generality as a primary target. We apply this strategy to the Pictet-Spengler condensation, for which we curate a database of 820 reactions, used to train statistical models of selectivity and activity. Starting from OSCAR, we define a combinatorial space of millions of catalyst possibilities, and perform evolutionary experiments on a diverse substrate scope that is representative of the whole chemical space of tetrahydro-β-carboline products. While privileged catalysts emerge, we show how genetic optimization can address the broader question of generality in asymmetric synthesis, extracting structure-performance relationships from the challenging areas of chemical space.

Application of Proline-Derived (Thio)squaramide Organocatalysts in Asymmetric Diels–Alder and Conjugate Addition Reactions

The synthesis of chiral proline-derived squaramide and thiosquaramide organocatalysts, which are capable of the dual activation in asymmetric reactions is reported. The (thio)squaramide moiety can form hydrogen bonds to activate the substrates and to stereocontrol the reaction, while the pyrrolidine unit can form enamines to activate carbonyl compounds via aminocatalysis. Comparing the performance of thiosquaramide to squaramide, the Diels–Alder reaction of (anthracen-9-yl)acetaldehyde and trans-β-nitrostyrene was examined, which has been investigated in the literature using quantum chemical calculations. Both squaramide and thiosquaramide gave excellent yields (up to 99%) and enantiomeric excess values (up to 98%). Moreover, their catalytic performance was compared in conjugate addition of lawsone to β,γ-unsaturated α-keto ester.

Harvesting the fragment-based nature of bifunctional organocatalysts to enhance their activity

Enhancing the activity of bifunctional organocatalysts: a fragment-based approach coupled with activity maps helps identifying better-performing catalytic motifs.

Non-Covalent Interactions in Enantioselective Organocatalysis: Theoretical and Mechanistic Studies of Reactions Mediated by Dual H-Bond Donors, Bifunctional Squaramides, Thioureas and Related Catalysts

Chiral bifunctional dual H-bond donor catalysts have become one of the pillars of organocatalysis. They include squaramide, thiosquaramide, thiourea, urea, and even selenourea-based catalysts combined with chiral amines, cinchona alkaloids, sulfides, phosphines and more. They can promote several types of reactions affording products in very high yields and excellent stereoselectivities in many cases: conjugate additions, cycloadditions, the aldol and Henry reactions, the Morita–Baylis–Hilman reaction, even cascade reactions, among others. The desire to understand mechanisms and the quest for the origins of stereoselectivity, in attempts to find guidelines for developing more efficient catalysts for new transformations, has promoted many mechanistic and theoretical studies. In this review, we survey the literature published in this area since 2015.

Diaminomethylenemalononitriles and Diaminomethyleneindanediones as Dual Hydrogen Bond Donors for Anion Recognition

Diaminomethylenemalononitriles (DMMs) and diaminomethyleneindanediones (DMIs) are dual H-bond donors that have previously been used as organocatalysts, but their anion binding ability has not been investigated. We report the synthesis of both alkyl- and aryl-substituted DMMs and DMIs, together with a comparison of their anion binding ability with that of the analogous thioureas. The DMMs display affinity for monovalent anions, with similar anion binding affinities observed to that of the thioureas in acetonitrile, albeit with differing trends for the N,N'-dialkyl versus N,N'-diaryl compounds. In contrast, the DMIs do not bind to monovalent anions under similar conditions as a result of conformational locking through the formation of intramolecular H-bonds. This can be overcome upon addition of sulfate ions, and binding of sulfate is enhanced in a more competitive solvent (DMSO).

N,N-Diacylaminals as Emerging Tools in Synthesis: From Peptidomimetics to Asymmetric Catalysis

N,N-Diacylaminals are flexible molecular scaffolds that have commonly been utilized as amide surrogates in peptidomimetics. The singularities of this motif as an N-acyl imine equivalent and as hydrogen-bond donor have recently opened new synthetic opportunities, especially in the field of asymmetric catalysis. This concept article highlights this diverse synthetic potential and provides the elements necessary for further developments.

Anion Binding Affinity: Acidity versus Conformational Effects

High-level quantum chemical calculations were used to elucidate the gas- and solution-phase conformational equilibria for a series of symmetrically substituted (thio)ureas, (thio)squaramides, and croconamides. Gas-phase calculations predict that the thermodynamic conformer of many of these anion receptors is not the dual-hydrogen-bond-facilitating anti-anti conformer as is commonly assumed. For N,N'-diaryl thiosquaramides and croconamides, the syn-syn conformer is typically the predominant conformer. Solution-phase calculations show that the anti-anti conformer is increasingly stabilized as the polarity of the solvent increases. However, the syn-syn conformer remains the lowest energy conformation for croconamides. These predictions are used to explain the acidity versus chloride binding affinity correlations recently reported for some of these compounds. The chloride binding constants for thioureas and croconamides are significantly lower than expected on the basis of their pK_a values, and this may be due in part to the need for these receptors to reorganize into the anti-anti conformer. Experimental NMR nuclear Overhauser effect (NOE) measurements of an asymmetrically substituted squaramide and its thio analogue are consistent with the syn-syn conformation being predominant at 298 K. The conformational equilibria should therefore be an important consideration for the design and development of future anion receptors and organocatalysts.

Organocatalysis and Beyond: Activating Reactions with Two Catalytic Species

Since the beginning of the millennium, organocatalysis has been gaining a predominant role in asymmetric synthesis and it is, nowadays, a foundation of catalysis. Synergistic catalysis, combining two or more different catalytic cycles acting in concert, exploits the vast knowledge acquired in organocatalysis and other fields to perform reactions that would be otherwise impossible. Merging organocatalysis with photo-, metallo- and organocatalysis itself, researchers have ingeniously devised a range of activations. This feature review, focusing on selected synergistic catalytic approaches, aims to provide a flavor of the creativity and innovation in the area, showing ground-breaking examples of organocatalysts, such as proline derivatives, hydrogen bond-mediated, Cinchona alkaloids or phosphoric acids catalysts, which work cooperatively with different catalytic partners.

Comparison of Cinchona Catalysts Containing Ethyl or Vinyl or Ethynyl Group at Their Quinuclidine Ring

Numerous cinchona organocatalysts with different substituents at their quinuclidine unit have been described and tested, but the effect of those saturation has not been examined before. This work presents the synthesis of four widely used cinchona-based organocatalyst classes (hydroxy, amino, squaramide, and thiourea) with different saturation on the quinuclidine unit (ethyl, vinyl, ethynyl) started from quinine, the most easily available cinchona derivative. Big differences were found in basicity of the quinuclidine unit by measuring the pKa values of twelve catalysts in six solvents. The effect of differences was examined by testing the catalysts in Michael addition reaction of pentane-2,4-dione to trans-β-nitrostyrene. The 1.6-1.7 pKa deviation in basicity of the quinuclidine unit did not result in significant differences in yields and enantiomeric excesses. Quantum chemical calculations confirmed that the ethyl, ethynyl, and vinyl substituents affect the acid-base properties of the cinchona-thiourea catalysts only slightly, and the most active neutral thione forms are the most stable tautomers in all cases. Due to the fact that cinchonas with differently saturated quinuclidine substituents have similar catalytic activity in asymmetric Michael addition application of quinine-based catalysts is recommended. Its vinyl group allows further modifications, for instance, recycling the catalyst by immobilization.

New enantiopure binaphthyl-cinchona thiosquaramides: synthesis and application for enantioselective organocatalysis

Binaphthyl-cinchona squaramide and thiosquaramide were applied as organocatalysts in three types of asymmetric reactions with excellent yields and enantioselectivities.

Carrying pieces of information in organocatalytic bytes: Semiopoiesis-A new theory of life and its origins

Living beings have been classically described as autopoietic machines: chemical systems, which maintain a reproducible steady state by producing their components and boundaries. On the other hand, very simple autopoietic micelles have been produced in laboratory. They consist in micelles able to catalyse the production of their own surfactants. However is very clear that these autopoietic systems are unable to evolve. In this way, these autopoietic micelles cannot be associated to living organisms, which are always linked by evolutionary relationships. Here I claim that living beings are a class of autopoietic systems able to conserve molecular information, a feature denoted by the term semiopoiesis. By defining the molecular information of their products, semiopoietic systems control their interaction with the medium and, by being able to convey molecular information beneficial to the maintenance of the organization to their offspring, semiopoietic systems can evolve by natural selection. Information can be described as a specific state or order assumed among a set of other possible states or orders. Thus, molecular information is the specific order by which the molecular components are ordered, such as the sequence of nucleotides in nucleic acids or of amino acids in proteins. However, molecular information is not limited to copolymers. The atoms in small organic compounds may also present diverse orders, giving rise to isomers. Different isomers can present very distinct chemical and physical properties such that the biophysical-chemical properties of an organic compound are determined by its composition and molecular information i.e. the specific positions in which their atoms are posited. This molecular information can be conserved during reactions catalysed by selective organocatalysts. In this way, organocatalysts appear as plausible candidates to primitive hosts for the genetic information, before the emergence of systems based in biopolymers. The bases of a putative organocatalysts-based evolution are discussed. Finally, I argue that organocatalytic micelles can be designed to produce programmable materials, artificial photosynthesis, self-building materials and artificial life with relevant industrial impact.

Development of Chiral, Bifunctional Thiosquaramides: Enantioselective Michael Additions of Barbituric Acids to Nitroalkenes

We report a general method for the synthesis of chiral thiosquaramides, a class of bifunctional catalysts not previously described in the literature. Thiosquaramides are found to be more acidic and significantly more soluble in nonpolar solvents than their oxosquaramide counterparts, and they are excellent catalysts for the unreported, enantioselective conjugate addition reaction of the barbituric acid pharmacaphore to nitroalkenes, delivering the chiral barbiturate derivatives in high yields and high enantioselectivities, even with catalyst loadings as low as 0.05 mol%.

Mechanism and Origins of Stereoselectivity in the Cinchona Thiourea- and Squaramide-Catalyzed Asymmetric Michael Addition of Nitroalkanes to Enones

We report density functional theory calculations that examine the mechanism and origins of stereoselectivity of Soós' landmark discovery from 2005 that cinchona thioureas catalyze the asymmetric Michael addition of nitroalkanes to enones. We show that the electrophile is activated by the catalyst's protonated amine and that the nucleophile binds to the thiourea moiety by hydrogen bonding. These results lead to the correction of published mechanistic work which did not consider this activation mode. We have also investigated the corresponding cinchona squaramide-catalyzed reaction and found that it proceeds by the same mechanism despite the differences in the geometry of the two catalysts' hydrogen-bond-donating groups, which demonstrates the generality of this mechanistic model.

Kinetic Analysis and Mechanism of the Hydrolytic Degradation of Squaramides and Squaramic Acids

The hydrolytic degradation of squaramides and squaramic acids, the product of partial hydrolysis of squaramides, has been evaluated by UV spectroscopy at 37 °C in the pH range 3-10. Under these conditions, the compounds are kinetically stable over long time periods (>100 days). At pH >10, the hydrolysis of the squaramate anions shows first-order dependence on both squaramate and OH^-. At the same temperature and [OH^-], the hydrolysis of squaramides usually displays biphasic spectral changes (A → B → C kinetic model) with formation of squaramates as detectable reaction intermediates. The measured rates for the first step (k₁ ≈ 10^-4 M^-1 s^-1) are 2-3 orders of magnitude faster than those for the second step (k₂ ≈ 10^-6 M^-1 s^-1). Experiments at different temperatures provide activation parameters with values of ΔH^⧧ ≈ 9-18 kcal mol^-1 and ΔS^⧧ ≈ -5 to -30 cal K^-1 mol^-1. DFT calculations show that the mechanism for the alkaline hydrolysis of squaramic acids is quite similar to that of amides.

Mechanistic Insights into the Mode of Action of Bifunctional Pyrrolidine-Squaramide-Derived Organocatalysts

The catalytic modes of action of three squaramide-derived bifunctional organocatalysts have been investigated using DFT methods. The [5+2] cycloaddition between oxidopyrylium ylides and enals was used as the model reaction. Two primary modes were possible for the different catalysts studied. The preference for one mode over the other was due to the possibility of additional favorable π-π interactions between the hydrogen-bond activated pyrylium ylide and an electron-deficient aromatic ring bonded to the squaramide NH group. The model can be extended to other reactions catalyzed by the same catalysts, such as formal [2+2] cycloadditions between nitroalkenes and α,β-unsaturated aldehydes. The computational results were in excellent concurrence with the available experimental reports on the observed total enantioselectivity and differences in diastereoselectivity depending on the substrate and the reaction.

Experimental and Theoretical Studies in Hydrogen-Bonding Organocatalysis

Chiral thioureas and squaramides are among the most prominent hydrogen-bond bifunctional organocatalysts now extensively used for various transformations, including aldol, Michael, Mannich and Diels-Alder reactions. More importantly, the experimental and computational study of the mode of activation has begun to attract considerable attention. Various experimental, spectroscopic and calculation methods are now frequently used, often as an integrated approach, to establish the reaction mechanism, the mode of activation or explain the stereochemical outcome of the reaction. This article comprises several case studies, sorted according to the method used in their study. The aim of this review is to give the investigators an overview of the methods currently utilized for mechanistic investigations in hydrogen-bonding organocatalysis.

The activation strain model and molecular orbital theory

The activation strain model is a powerful tool for understanding reactivity, or inertness, of molecular species. This is done by relating the relative energy of a molecular complex along the reaction energy profile to the structural rigidity of the reactants and the strength of their mutual interactions: ΔE(ζ) = ΔE_strain(ζ) + ΔE_int(ζ). We provide a detailed discussion of the model, and elaborate on its strong connection with molecular orbital theory. Using these approaches, a causal relationship is revealed between the properties of the reactants and their reactivity, e.g., reaction barriers and plausible reaction mechanisms. This methodology may reveal intriguing parallels between completely different types of chemical transformations. Thus, the activation strain model constitutes a unifying framework that furthers the development of cross-disciplinary concepts throughout various fields of chemistry. We illustrate the activation strain model in action with selected examples from literature. These examples demonstrate how the methodology is applied to different research questions, how results are interpreted, and how insights into one chemical phenomenon can lead to an improved understanding of another, seemingly completely different chemical process. WIREs Comput Mol Sci 2015, 5:324-343. doi: 10.1002/wcms.1221.

Turning on catalysis: incorporation of a hydrogen-bond-donating squaramide moiety into a Zr metal-organic framework

Herein, we demonstrate that the incorporation of an acidic hydrogen-bond-donating squaramide moiety into a porous UiO-67 metal-organic framework (MOF) derivative leads to dramatic acceleration of the biorelevant Friedel-Crafts reaction between indole and β-nitrostyrene. In comparison, it is shown that free squaramide derivatives, not incorporated into MOF architectures, have no catalytic activity. Additionally, using the UiO-67 template, we were able to perform a direct comparison of catalytic activity with that of the less acidic urea-based analogue. This is the first demonstration of the functionalization of a heterogeneous framework with an acidic squaramide derivative.

A squaramide and tertiary amine: an excellent hydrogen-bonding pair organocatalyst for living polymerization

A hydrogen-bond motif based on a squaramide and sparteine efficiently promoted the ring-opening polymerization of l-lactide at ambient temperature.

Enantioselective selenocyclization via dynamic kinetic resolution of seleniranium ions by hydrogen-bond donor catalysts

Highly enantioselective selenocyclization reactions are promoted by the combination of a new chiral squaramide catalyst, a mineral acid, and an achiral Lewis base. Mechanistic studies reveal that the enantioselectivity originates from the dynamic kinetic resolution of seleniranium ions through anion-binding catalysis.

Toward a more complete understanding of noncovalent interactions involving aromatic rings

Noncovalent interactions involving aromatic rings, which include π-stacking interactions, anion-π interactions, and XH-π interactions, among others, are ubiquitous in chemical and biochemical systems. Despite dramatic advances in our understanding of these interactions over the past decade, many aspects of these noncovalent interactions have only recently been uncovered, with many questions remaining. We summarize our computational studies aimed at understanding the impact of substituents and heteroatoms on these noncovalent interactions. In particular, we discuss our local, direct interaction model of substituent effects in π-stacking interactions. In this model, substituent effects are dominated by electrostatic interactions of the local dipoles associated with the substituents and the electric field of the other ring. The implications of the local nature of substituent effects on π-stacking interactions in larger systems are discussed, with examples given for complexes with carbon nanotubes and a small graphene model, as well as model stacked discotic systems. We also discuss related issues involving the interpretation of electrostatic potential (ESP) maps. Although ESP maps are widely used in discussions of noncovalent interactions, they are often misinterpreted. Next, we provide an alternative explanation for the origin of anion-π interactions involving substituted benzenes and N-heterocycles, and show that these interactions are well-described by simple models based solely on charge-dipole interactions. Finally, we summarize our recent work on the physical nature of substituent effects in XH-π interactions. Together, these results paint a more complete picture of noncovalent interactions involving aromatic rings and provide a firm conceptual foundation for the rational exploitation of these interactions in a myriad of chemical contexts.

Organocatalytic enantio- and diastereoselective conjugate addition to nitroolefins: when β-ketoamides surpass β-ketoesters

Our findings on the bifunctional squaramide-catalyzed enantioselective conjugate addition of β-ketoamides to nitroolefins are disclosed. It appears that simple acyclic methylene β-ketoamides, unlike the extensively studied β-ketoesters, afford the products in excellent diastereoselectivities, and maintain high yields and enantioselectivities. Moreover, competition and kinetic studies were conducted to rationalize the observed reactivity and selectivity. The high level of diastereocontrol, along with the amenability of the amide group to postfunctionalization, dramatically increase the synthetic usefulness of the transformation.

On the mechanism of bifunctional squaramide-catalyzed organocatalytic Michael addition: a protonated catalyst as an oxyanion hole

A joint experimental-theoretical study of a bifunctional squaramide-amine-catalyzed Michael addition reaction between 1,3-dioxo nucleophiles and nitrostyrene has been undertaken to gain insight into the nature of bifunctional organocatalytic activation. For this highly stereoselective reaction, three previously proposed mechanistic scenarios for the critical CC bond-formation step were examined. Accordingly, the formation of the major stereoisomeric products is most plausible by one of the bifunctional pathways that involve electrophile activation by the protonated amine group of the catalyst. However, some of the minor product isomers are also accessible through alternative reaction routes. Structural analysis of transition states points to the structural invariance of certain fragments of the transition state, such as the protonated catalyst and the anionic fragment of approaching reactants. Our topological analysis provides deeper insight and a more general understanding of bifunctional noncovalent organocatalysis.

Asymmetric Synthesis of Functionalized Dihydro- and Tetrahydropyrans via an Organocatalytic Domino Michael-Hemiacetalization Reaction

Starting from α-hydroxymethyl nitroalkenes and various 1,3-dicarbonyl compounds, a one-pot organocatalyzed diastereo- and enantioselective synthesis of polyfunctionalized dihydro- and tetrahydropyran derivatives via a domino Michael-hemiacetalization sequence is reported. The title compounds bearing a variety of functional groups can be synthesized in this way in good yields (59-91%) and with moderate to excellent diastereoselectivities (26-98% de) and enantioselectivities (71-99% ee).

Performance of DFT methods and origin of stereoselectivity in bipyridine N,N′-dioxide catalyzed allylation and propargylation reactions

It is shown that many DFT methods correctly predict the stereoselectivity of bipyridine N,N′-dioxide catalyzed alkylation reactions despite predicting the incorrect low-lying transition state structures. A novel explanation of the origin of stereoselectivity in these reactions is also provided.

Thiosquaramides: pH switchable anion transporters

The transport of anions across cellular membranes is an important biological function governed by specialised proteins. In recent years, many small molecules have emerged that mimick the anion transport behaviour of these proteins, but only a few of these synthetic molecules also display the gating/switching behaviour seen in biological systems. A small series of thiosquaramides was synthesised and their pH-dependent chloride binding and anion transport behaviour was investigated using ¹H NMR titrations, single crystal X-ray diffraction and a variety of vesicle-based techniques. Spectrophotometric titrations and DFT calculations revealed that the thiosquaramides are significantly more acidic than their oxosquaramide analogues, with pK_a values between 4.0 and 9.0. This led to the observation that at pH 7.2 the anion transport ability of the thiosquaramides is fully switched OFF due to deprotonation of the receptor, but is completely switched ON at lower pH.

Hydrogen bond donor–acceptor–donor organocatalysis for conjugate addition of benzylidene barbiturates via complementary DAD–ADA hydrogen bonding

Organocatalysts featuring a hydrogen bond donor–acceptor–donor structural element catalyze conjugate addition via complementary DAD–ADA hydrogen bonding.