Mechanistic Insights into Bicyclic Guanidine-Catalyzed Reactions from Microscopic and Macroscopic Perspectives

In silico investigation on the separation of disulfide bonds by N-heterocyclic carbene

Herein, the separation of a disulfide bond using different nucleophilic agents like tri-methyl phosphine (TMP), tris (2-carboxyethyl) phosphine (TCEP), and N-heterocyclic carbene (NHC) has been investigated. Both TMP and TCEP have demonstrated their ability to break disulfide bonds through the SN2 mechanism. However, it is worth noting that these reactions are endothermic. While searching for a suitable nucleophile, it was observed that the NHC-mediated reaction was exothermic. The natural bond orbital (NBO), principal interacting orbital (PIO) and extended transition state-natural orbitals for chemical valence (ETS-NOCV) studies help understand the electron transfer process between interacting orbitals during the chemical reactions.

Mechanisms and Stereoselectivities in the NHC-Catalyzed [4 + 2] Annulation of 2-Bromoenal and 6-Methyluracil-5-carbaldehyde

To disclose the reaction mechanism and selectivity in the NHC-catalyzed reaction of 2-bromoenal and 6-methyluracil-5-carbaldehyde, a systematic computational study has been performed. According to DFT computations, the catalytic cycle is divided into eight elementary steps: nucleophilic attack of the NHC on 2-bromoenal, 1,2-proton transfer, C-Br bond dissociation, 1,3-proton transfer, addition to 6-methyluracil-5-carbaldehyde, [2 + 2] cycloaddition, NHC dissociation, and decarboxylation. The Bronsted acid DABCO·H+ plays a crucial role in proton transfer and decarboxylation steps. The addition to 6-methyluracil-5-carbaldehyde determines both chemoselectivity and stereoselectivity, leading to R-configured carbocycle-fused uracil, in agreement with experimental results. NCI analysis indicates that the CH···N, CH···π, and LP···π interactions should be the key factor for determining the stereoselectivity. ELF analysis shows the main role of the NHC in promoting C-Br bond dissociation. The mechanistic insights obtained in the present work may guide the rational design of potential NHC catalysts.

A Practical and Robust Zwitterionic Cooperative Lewis Acid/Acetate/Benzimidazolium Catalyst for Direct 1,4-Additions

A catalyst type is disclosed allowing for exceptional efficiency in direct 1,4-additions. The catalyst is a zwitterionic entity, in which acetate binds to Cu^II , which is formally negatively charged and serving as counterion for benzimidazolium. All 3 functionalities are involved in the catalytic activation. For maleimides productivity was increased by a factor >300 compared to literature (TONs up to 6700). High stereoselectivity and productivity was attained for a broad range of other Michael acceptors as well. The polyfunctional catalyst is accessible in only 4 steps from N-Ph-benzimidazole with an overall yield of 96 % and robust during catalysis. This allowed to reuse the same catalyst multiple times with nearly constant efficiency. Mechanistic studies, in particular by DFT, give a detailed picture how the catalyst operates. The benzimidazolium unit stabilizes the coordinated enolate nucleophile and prevents that acetate/acetic acid dissociate from the catalyst.

Molecular Understanding and Practical In Silico Catalyst Design in Computational Organocatalysis and Phase Transfer Catalysis-Challenges and Opportunities

Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed.

Organocatalyzed Phospha-Michael Addition: A Highly Efficient Synthesis of Customized Bis(acyl)phosphane Oxide Photoinitiators

Addition of the P-H bond in bis(mesitoyl)phosphine, HP(COMes)₂ (BAPH), to a wide variety of activated carbon-carbon double bonds as acceptors was investigated. While this phospha-Michael addition does not proceed in the absence of an additive or catalyst, excellent results were obtained with stoichiometric basic potassium or caesium salts. Simple amine bases can be employed in catalytic amounts, and tetramethylguanidine (TMG) in particular is an outstanding catalyst that allows the preparation of bis(acyl)phosphines, R-P(COMes)₂ , under very mild conditions in excellent yields after only a short time. All phosphines RP(COMes)₂ can subsequently be oxidized to the corresponding bis(acyl)phosphane oxides, RPO(COMes)₂ , a substance class belonging to the most potent photoinitiators for radical polymerizations known to date. Thus, a simple and highly atom economic method has been found that allows the preparation of a broad range of photoinitiators adapted to their specific field of application even on a large scale.

Three-Dimensional Quantitative Structure and Activity Relationship of Flavones on Their Hypochlorite Scavenging Capacity

Flavonoids, a class of polyphenolic substances widely present in the plant realm, are considered as ideal hypochlorite scavengers. However, to our knowledge, little study has focused on the structure-activity relationship between flavonoids and hypochlorite scavenging capacity. Herein, we report for the first time the three-dimensional quantitative structure and activity relationship (3D-QSAR) combined with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Four models derived from CoMFA and CoMSIA with different combinations of descriptors were built and compared; the CoMFA model, which included both steric and electrostatic fields, showed great potential (R² = 0.989; Q² = 0.818) in predictive quality according to both internal and external validation criteria. Additionally, the average local ionization energy (ALIE), electrostatic potential (ESP), and orbital weighted dual descriptor (OWDD) were determined to identify the key structural moiety for scavenging capacity of flavonoids against hypochlorite. The computational results indicated that hypochlorous acid (HClO) serves as an electrophile undergoing electrophilic addition to the C6 carbon, which has the highest negative charge density, which are influenced by the functional groups on the flavones. The DFT calculated mechanism revealed the catalytic role of water of mono- and di-chlorination reactions, characterized by low activation barriers, and the involvement of neutral, instead of high-energy carbocation, intermediates.

A DFT study of NHC-catalyzed reactions between 2-bromo-2-enals and acylhydrazones: mechanisms, and chemo- and stereoselectivities

The reaction mechanisms and origins of the chemo- and stereoselectivities of NHC-catalyzed [4 + 2] annulation of 2-bromo-2-enals and acylhydrazones.

Exploring the Effects of Water on the Mechanism of the Catalyst-Free Reaction between Isatin and 3-Methyl-2-pyrazolin-5-one from the Mixed Implicit/Explicit Multiple Types of Water Clusters

Density functional theory calculations with implicit/explicit water cluster models were conducted to pursue deeper understandings about the mechanism and the water effects in the reaction of isatin with 3-methyl-2-pyrazolin-5-one. The proposed preferential mechanistic scenario here undergoes three major steps: first, 3-methyl-2-pyrazolin-5-one converts to its enol form and then, the aldol addition reaction takes place between isatin and enol to generate the intermediate INT2, followed finally by the tautomerization of INT2 to become the product 3-pyrazolone. The computed results indicate that the direct aldol reaction without the water auxiliary is feasible in the second step and the remaining tautomerization steps (steps 1, 3, and 4) assisted by tri-, tri-, and six-water cluster models, respectively, are the most favorable cases. It is further noted that more hydrogen bonding interactions in the tri-water auxiliary reaction are essential for the reduction of the free energy barrier ΔG^⧧ in the proton transfer largely than those assisted by the other types of water cluster models. The origin of the more stable transition state in the rate-determining step of the tri-water cluster model is ascribed to smaller cyclic strain and more global electron density transfer associated to its structure than the other types of water cluster models.

1,1-Diaminoazines as organocatalysts in phospha-Michael addition reactions

1,1-Diaminoazines can act as effective organocatalysts for the formation of phosphorus-carbon bonds between biphenylphosphine oxide and an activated alkene (Michael acceptor). These catalysts provide the P-C adducts at a faster rate and with relatively better yields in comparison to the organocatalysts employed earlier. The notable advantage is that 1,1-diaminoazines catalyse the reaction even in an aqueous medium with very good yields. Organocatalysis using 1,1-diaminoazines was also successfully carried out between dimethylphosphite and benzylidenemalononitrile under multicomponent conditions.

Guanidine-Amide-Catalyzed Aza-Henry Reaction of Isatin-Derived Ketimines: Origin of Selectivity and New Catalyst Design

Density functional theory (DFT) calculations were performed to investigate the mechanism and the enantioselectivity of the aza-Henry reaction of isatin-derived ketimine catalyzed by chiral guanidine–amide catalysts at the M06-2X-D3/6-311+G(d,p)//M06-2X-D3/6-31G(d,p) (toluene, SMD) theoretical level. The catalytic reaction occurred via a three-step mechanism: (i) the deprotonation of nitromethane by a chiral guanidine–amide catalyst; (ii) formation of C–C bonds; (iii) H-transfer from guanidine to ketimine, accompanied with the regeneration of the catalyst. A dual activation model was proposed, in which the protonated guanidine activated the nitronate, and the amide moiety simultaneously interacted with the ketimine substrate by intermolecular hydrogen bonding. The repulsion of CPh₃ group in guanidine as well as N-Boc group in ketimine raised the Pauli repulsion energy (∆E_Pauli) and the strain energy (∆E_strain) of reacting species in the unfavorable si-face pathway, contributing to a high level of stereoselectivity. A new catalyst with cyclopropenimine and 1,2-diphenylethylcarbamoyl as well as sulfonamide substituent was designed. The strong basicity of cyclopropenimine moiety accelerated the activation of CH₃NO₂ by decreasing the energy barrier in the deprotonation step. The repulsion between the N-Boc group in ketimine and cyclohexyl group as well as chiral backbone in the new catalyst raised the energy barrier in C–C bond formation along the si-face attack pathway, leading to the formation of R-configuration product. A possible synthetic route for the new catalyst is also suggested.

Mechanism and regio- and stereoselectivity in an NHC-catalyzed Mannich/lactamization domino reaction

Density functional theory (DFT) calculations (M06-2X) have been employed to disclose the mechanisms and regio- and stereo-selectivities of the N-heterocyclic carbene (NHC)-catalyzed reaction of 2-benzothiazolimines and α-chloroaldehydes. The preferred mechanism is initiated by the nucleophilic attack of NHC on α-chloroaldehyde (first step), followed by 1,2-proton transfer which was assisted by the Brønsted acid DABCO·H+ to generate the Breslow intermediate (second step). The cleavage of the C-Cl bond (third step) and deprotonation (fourth step) form the enolate intermediate. This further reacts with 2-benzothiazolimine which leads to the formation of a new C-C bond (fifth step). Subsequent cyclization takes place via the formation of a new C-N bond (sixth step). Catalyst regeneration completes the whole catalytic cycle and affords the final product (seventh step). The DFT results indicate that the fifth step determines the stereochemistry of the reaction and leads to benzothiazolopyrimidinone with the SS configuration, which agrees well with experimental observations. Intramolecular cyclization is found to be the regioselectivity-determining step, for which the [4+2] annulation pathway is more preferred than that via [2+2] annulation, which again agrees well with experimental observations. Based on the mechanism proposed, the origins of regio- and stereoselectivities have also been investigated by performing distortion/interaction, natural bond orbital (NBO) and non-covalent interaction (NCI) analyses. The mechanistic insights gained in this work should be helpful in the rational design of potential catalysts for analogous reactions.

Mechanistic study on the NHC-catalyzed [3+4] annulation of enals and thiazolones

Reaction mechanisms and origins of regio- and stereo-selectivities of NHC catalyzed [3+4] annulation of enals and thiazolones.

Bicyclic Guanidine-Catalyzed Asymmetric Cycloaddition Reaction of Anthrones-Bifunctional Binding Modes and Origin of Stereoselectivity

We report a computational analysis of the [5,5] bicyclic guanidine-catalyzed asymmetric cycloaddition reaction of anthrones. Based on extensive conformational search of key intermediates and transition states on the potential energy surface and density functional theory calculations, we studied five plausible binding modes between the guanidine catalyst and substrates for this reaction. Our results indicate that the most favorable pathway is a stepwise conjugate addition-Aldol sequence via the dual hydrogen-bond binding mode. The predicted level of enantioselectivity is in good agreement with experimental values. Trends in variation of substrates and catalysts have also been reproduced by our calculations. Decomposition analysis revealed the significance of aromatic interactions in stabilizing the key enantioselectivity-determining transition state structures.

Transition metal-free functionalized hydration of alkynes: one-pot synthesis of fluorinated β-keto-imidates using Selectfluor

A transition metal-free, four-component one-pot synthesis of polyfunctionalized fluorinated β-keto-imidates via the functionalized hydration of alkynes has been described. The intermediate 1,3-ketoamino moiety was obtained from easily accessible arylpropioladehyde and arlyhydroxylamine and was treated with Selectfluor delivering fluorinated β-keto-imidates. A wide variety of functional groups are tolerated under mild reaction conditions and the product applicability is highlighted.

Mechanism and stereoselectivity in NHC-catalyzed β-functionalization of saturated carboxylic ester

To understand the mechanism and origin of the stereoselectivity of the [3 + 2] annulation reaction between a carboxylic ester and an isatin generating spirooxindole lactone catalyzed by N-heterocyclic carbene (NHC), density functional theory (DFT) calculations have been carried out. DFT results indicate that the catalytic cycle begins with the coupling of the catalyst with benzotriazole ester, followed by α-deprotonation to produce the enolate intermediate. The subsequent 1,4-proton transfer affords the homoenolate intermediate. The next crucial step is the stereoselective C-C bond formation. Then proton transfer takes place leading to the formation of the lactone intermediate. Finally, the elimination of the catalyst furnishes the final product. The presence of 1-hydroxybenzotriazole (HOBt) dramatically accelerates the proton transfer step. More importantly, HOBt has a non-negligible impact on stereoselective C-C bond formation, and the SR-configured product is the major stereoisomer of the annulation product, which is in good agreement with the experimental observations. The differential π⋯π stacking, C-H⋯π, lone pair (LP)⋯π and repulsion interactions are found to be responsible for the stereoselectivity. The obtained mechanistic insights should provide valuable information for understanding the important roles of the NHC catalyst and HOBt additive and be helpful for designing better NHC catalysts for this kind of reaction.

Understanding the mechanism and stereoselectivity of NHC-catalyzed [3 + 2] cycloaddition of 3-bromoenals and isatin N-Boc ketimines

The mechanism and origin of stereoselectivities in N-heterocyclic carbine (NHC)-catalyzed [3 + 2] cycloaddition of 3-bromoenals and isatin N-Boc ketimines have been studied using density functional theory (DFT) calculations. Various possible reaction pathways were examined and analyzed. Our calculation results reveal that the catalytic cycle can be characterized by six steps: nucleophilic attack of a catalyst on 3-bromoenal (step I); [1,2]-proton transfer (step II); addition to the other reactant isatin N-Boc ketimine (step III); debromination (step IV); intramolecular cycloaddition concerted with hydrogen-elimination (step V) and elimination of the NHC catalyst (step VI). For step II, besides the direct [1,2]-proton transfer, the mediator (base and water)-assisted proton transfer has been investigated, and the DFT results show that the 2H2O cluster-mediated proton transfer is most energy favorable. The carbon-carbon bond formation step (step III) is calculated to be the stereoselectivity-determining step and the S-configuration product is the predominant product, which are in good agreement with the experimental observations. The mechanistic insights gained in this work should be helpful for other NHC-catalyzed reactions.

Mechanisms of phosphine-catalyzed [3+3] cycloaddition of ynones and azomethine imines: a DFT study

Mechanisms of PPh₃-catalyzed [3+3] cycloaddition between a ynone and an azomethine imine.

Chiral guanidines and their derivatives in asymmetric synthesis

This article reviews current achievements of chiral guanidines and their derivatives in organocatalysis, and updates versatile guanidine–metal salt combinations in asymmetric catalytic reactions.

Gold-catalyzed Fluorination of Alkynyl Esters and Ketones: Efficient Access to Fluorinated 1,3-Dicarbonyl Compounds

We developed an efficient synthesis of 2-fluoro-1,3-dicarbonyl compounds using readily available alkynyl ketones or esters as starting material. The key step is the insertion of hydrogen fluoride (HF) to the gold carbene intermediate generated from cationic gold catalyzed addition of N-oxides to alkynyl ketones or esters. This method gives excellent chemical yields and regioselectivity with good functional group tolerance.

Mechanistic investigation on N → Cα → O relay via non-Brook rearrangement: reaction conditions promote synthesis of furo[3,2-c]pyridinones

A comprehensive density functional theory investigation was employed to disclose the effect of reaction conditions on the mechanism and effective anion relay sequence of a NaH promoted non-Brook rearrangement of benzaldehyde and 1-cinnamoylcyclopropanecarboxamides. Two main mechanisms were explored under four different reaction conditions: Na⁺-assisted and nH₂O-Na⁺, 2H₂O-DMSO-Na⁺, and Na⁺-DMSO co-assisted, and the difference relies on the reaction sequence between the concerted ring-opening and recyclization and electrophilic addition. Being different from previous reports, a cooperative participation of water, solvent DMSO and counterion Na⁺ is revealed in the preferential mechanism. The preferred scenario undergoes five major steps: deprotonation, aza-Michael addition, electrophilic addition, NaOH elimination and a concerted ring-opening and recyclization step. The rate-determining step is the concerted ring-opening and recyclization process with an energy barrier of 30.2 kcal mol^-1. We found that the effective anion relay of a non-Brook rearrangement order is N → C^α → O rather than the previously proposed aza-oxy-carbanion. Meanwhile, a mixed type of ARC chemistry through a novel non-Brook rearrangement was disclosed. Moreover, the non-covalent interactions between substrate and reactant extensively affect the anion relay process by hydrogen-bonding (O-HO and C-HO) and electrostatic (Na⁺O) interactions. Thus, our results provide insightful clues to the mechanism of the reaction condition catalyzed non-Brook rearrangement reaction.

Coupling Reactions of Alkynyl Indoles and CO2 by Bicyclic Guanidine: Origin of Catalytic Activity?

Density functional theory calculations were used to investigate the three possible modes of activation for the coupling of CO₂ with alkynyl indoles in the presence of a guanidine base. The first of these mechanisms, involving electrophilic activation, was originally proposed by Skrydstrup et al. (Angew. Chem. Int. Ed. 2015, 54, 6682). The second mechanism involves the nucleophilic activation of CO₂ . Both of these electrophilic and nucleophilic activation processes involve the formation of a guanidine-CO₂ zwitterion adduct. We have proposed a third mechanism involving the bifunctional activation of the bicyclic guanidine catalyst, allowing for the simultaneous activation of the indole and CO₂ by the catalyst. We demonstrated that a second molecule of catalyst is required to facilitate the final cyclization step. Based on the calculated turnover frequencies, our newly proposed bifunctional activation mechanism is the most plausible pathway for this reaction under these experimental conditions. Furthermore, we have shown that this bifunctional mode of activation is consistent with the experimental results. Thus, this guanidine-catalyzed reaction favors a specific-base catalyzed mechanism rather than the CO₂ activation mechanism. We therefore believe that this bifunctional mechanism for the activation of bicyclic guanidine is typical of most CO₂ coupling reactions.

The chemistry and biology of guanidine natural products

The chemistry and biology of natural guanidines isolated from microbial culture media, from marine invertebrates, as well as from terrestrial plants and animals, are reviewed.

Mechanisms and stereoselectivities of the DABCO-catalyzed Rauhut–Currier reaction of α,β-unsaturated ketones and aryl acrylates: a computational investigation

Mechanism of the RC reaction in the absence and presence of PhOH.

Guanidine-catalyzed asymmetric Strecker reaction: modes of activation and origin of stereoselectivity

Density functional theory calculations were employed to study the catalytic mechanism, modes of activation, and origin of enantioselectivity of guanidine-catalyzed asymmetric Strecker reaction of N-benzhydryl imine with hydrogen cyanide. Two types of bifunctional activation mode were identified, namely conventional bifunctional Brønsted acid activation and unconventional bifunctional Brønsted–Lewis acid activation. The lowest-energy transition states correspond to the conventional bifunctional mode of activation. The calculated enantiomeric excess, based on eight lowest-energy C–C bond forming transition states, is in good accord with observed enantioselectivity. NCI (noncovalent interaction) analysis of the key transition states reveals extensive noncovalent interactions, including aromatic interactions and hydrogen bonds, between the guanidinium catalyst and substrates. Multiple aryl–aryl interactions between the phenyl groups of guanidine catalyst and the phenyl rings of N-benzhydryl imine are the key stabilizations in the most stable (R)-inducing transition state. Differential attractive aryl–aryl stabilization is the major factor for stereoinduction.

Enhanced Basicity of Push-Pull Nitrogen Bases in the Gas Phase

Nitrogen bases containing one or more pushing amino-group(s) directly linked to a pulling cyano, imino, or phosphoimino group, as well as those in which the pushing and pulling moieties are separated by a conjugated spacer (C═X)_n, where X is CH or N, display an exceptionally strong basicity. The n-π conjugation between the pushing and pulling groups in such systems lowers the basicity of the pushing amino-group(s) and increases the basicity of the pulling cyano, imino, or phosphoimino group. In the gas phase, most of the so-called push-pull nitrogen bases exhibit a very high basicity. This paper presents an analysis of the exceptional gas-phase basicity, mostly in terms of experimental data, in relation with structure and conjugation of various subfamilies of push-pull nitrogen bases: nitriles, azoles, azines, amidines, guanidines, vinamidines, biguanides, and phosphazenes. The strong basicity of biomolecules containing a push-pull nitrogen substructure, such as bioamines, amino acids, and peptides containing push-pull side chains, nucleobases, and their nucleosides and nucleotides, is also analyzed. Progress and perspectives of experimental determinations of GBs and PAs of highly basic compounds, termed as "superbases", are presented and benchmarked on the basis of theoretical calculations on existing or hypothetical molecules.

Base-Catalyzed Stereospecific Isomerization of Electron-Deficient Allylic Alcohols and Ethers through Ion-Pairing

A mild base-catalyzed strategy for the isomerization of allylic alcohols and allylic ethers has been developed. Experimental and computational investigations indicate that transition metal catalysts are not required when basic additives are present. As in the case of using transition metals under basic conditions, the isomerization catalyzed solely by base also follows a stereospecific pathway. The reaction is initiated by a rate-limiting deprotonation. Formation of an intimate ion pair between an allylic anion and the conjugate acid of the base results in efficient transfer of chirality. Through this mechanism, stereochemical information contained in the allylic alcohols is transferred to the ketone products. The stereospecific isomerization is also applicable for the first time to allylic ethers, yielding synthetically valuable enantioenriched (up to 97% ee) enol ethers.

First example of an organocatalytic asymmetric Mannich reaction between aldimines of glycinates and sulphonyl imines

The catalytic enantioselective Mannich-type reaction between glycinate Schiff base and imines has been one of the most efficient routes for accessing α,β-diamino acids. However, the glycinate Schiff bases used in the references were almost ketimines. Only several examples of aldimines were used in the presence of metal catalyst. We developed the first example of an asymmetric direct Mannich reaction using aldimines of glycinates instead of ketimines of glycinates. The reaction was well catalyzed by chiral guanidine with high yield (up to 92%) and moderate stereoselectivity (up to 65%).

Understanding the mechanisms, regioselectivies and enantioselectivities of the DMAP-catalyzed [2 + 4] cycloaddition of γ-methyl allenoate and phenyl(phenyldiazenyl)methanone

DMAP-catalyzed [2 + 4] cycloaddition reaction.

A theoretical study of DABCO and PPh3 catalyzed annulations of allenoates with azodicarboxylate

Previous experiments have shown that DABCO-catalyzed annulation of 2,3-butadienoate and diethylazodicarboxylate leads to 1,2-diazetidine (reaction (1)), whereas PPh3-catalyzed 2-benzyl-2,3-butadienoate and diethylazodicarboxylate gives pyrazoline (reaction (2)).