Attractive Noncovalent Interactions Research Articles

Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors.

Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy and is a severe condition with no treatment currently available. Recently, small-molecule ligands have been developed as targeted covalent inhibitors that have some selectivity for and covalently inhibit cyclin-dependent kinase 12 (CDK12). CDK12 is involved in the transcription of elongated RNA sections that results in the DM1 condition. The covalent bond is achieved after nucleophilic addition to a Michael acceptor warhead. Previous studies of the conformational preferences of thio-Michael additions have focused on characterizing the reaction profile based on the distance between the sulfur and β-carbon atoms. Rotamerism, however, has not been investigated extensively. Here, we use high-level quantum chemistry calculations, up to coupled cluster with single, double, and perturbative triple excitations [CCSD(T)], to characterize the nucleophilic addition of an archetypal nucleophile, methanethiolate, to various nitrogen-containing Michael acceptors which are representative of the small-molecule covalent inhibitors. By investigating the structural, energetic, and electronic properties of the resulting enolates, as well as their reaction profiles, we show that synclinal additions are generally energetically favored over other additions due to the greater magnitude of attractive noncovalent interactions permitted by the conformation. The calculated transition states associated with the addition process indicate that synclinal addition proceeds via lower energetic barriers than antiperiplanar addition and is the preferred reaction pathway.

The Role of Attractive Non-Covalent Interactions in Peptide Macrocyclization.

The efficiency of macrocyclization reactions relies on the appropriate conformational preorganization of a linear precursor, ensuring that reactive ends are in spatial proximity prior to ring closure. Traditional peptide cyclization approaches that reduce the extent of terminal ion pairing often disfavor cyclization-conducive conformations and can lead to undesired cyclodimerization or oligomerization side reactions, particularly when they are performed without high dilution. To address this challenge, synthetic strategies that leverage attractive noncovalent interactions, such as zwitterionic attraction between chain termini during macrocyclization, offer a potential solution by reducing the entropic penalty associated with linear peptides adopting precyclization conformations. In this study, we investigate the role of (N-isocyanoimino)triphenylphosphorane (Pinc) in facilitating the cyclization of linear peptides into conformationally rigid macrocycles. The observed moderate diastereoselectivity is consistent with the preferential Si-facial addition of Pinc, where the isocyanide adds to the E-iminium ion on the same face as the l-proline amide group. The resulting peptide chain reveals that the activated phosphonium ylide of Pinc brings the reactive ends close together, promoting cyclization by enclosing the carboxylate within the interior of the pentapeptide and preventing the formation of byproducts. For shorter peptides with modified peptide backbones, the cyclization mechanism and outcome are redirected, as nucleophilic motifs such as thiazole and imidazole can covalently trap nitrilium intermediates. The isolation of the intermediate in the unproductive macrocyclization pathway, along with nuclear magnetic resonance and density functional theory studies, provides insights into heterocycle-dependent selectivity. The Pinc-driven macrocyclization process has generated diverse collections of cyclic molecules, and our models offer a comprehensive understanding of observed trends, facilitating the development of other heterocycle-forming macrocyclization reactions.

Application of sSPhos as a Chiral Ligand for Palladium-Catalyzed Asymmetric Allylic Alkylation.

Palladium-catalyzed asymmetric allylic alkylation is a versatile method for C-C bond formation. Many established classes of chiral ligands can perform allylic alkylation reactions enantioselectively, but identification of new ligand classes remains important for future development of the field. We demonstrate that enantiopure sSPhos, a bifunctional chiral monophosphine ligand, when used as its tetrabutyl ammonium salt, is a highly effective ligand for a benchmark Pd-catalyzed allylic alkylation reaction. We explore the scope and limitations and perform experiments to probe the origin of selectivity. In contrast with reactions previously explored using enantiopure sSPhos, it appears that steric bulk around the sulfonate group is responsible for the high enantioselectivity in this case, rather than attractive noncovalent interactions.

Zwitterionic Aqua Palladacycles with Noncovalent Interactions for meta-Selective Suzuki Coupling of 3,4-Dichlorophenol and 3,4-Dichlorobenzyl Alcohol in Water.

The site-selective reaction of substrates with multiple reactive sites has been a focus of the current synthetic chemistry. The use of attractive noncovalent interactions between the catalyst and substrate is emerging as a versatile approach to address site-selectivity challenges. Herein, we designed and synthesized a series of palladacycles, to control meta-selective Suzuki coupling of 3,4-dichlorophenol and 3,4-dichlorobenzyl alcohol. Noncovalent interactions directed zwitterionic aqua palladacycles catalyzed meta-selective Suzuki couplings of 3,4-dichloroarenes bearing hydroxyl in water have been developed. Experiments and density functional theory (DFT) calculations demonstrated that the electrostatic interactions play a critical role in meta-selective coupling of 3,4-dichlorophenol, while meta-selective coupling of 3,4-dichlorobenzyl alcohol arises due to the hydrogen-bonding interactions.

MXenes quantum dots for efficient pesticide adsorbents: A first principal study of the adsorption capability

In the quest for environmental preservation, illness prevention, and food safety, the development of highly sensitive pesticide sensors is crucial. This study delves into the electronic properties, adsorption traits, reusability, and intermolecular interactions of Ti2C quantum dots and passivated Ti2C quantum dots regarding three hazardous pesticides: acetamiprid, atrazine, and bentazon. We explore both surface and edge configurations of these nanomaterials to assess their suitability for pesticide detection and removal. Adsorption energy estimates reveal the bond strength between quantum dots and pesticides. Ti2C quantum dots exhibit superior intermolecular bonding compared to Ti2CO quantum dots, promising efficient pesticide adsorption. Concerning reusability, Ti2CO quantum dots prove environmentally friendly and cost-effective due to their lower adsorption energy. Non-covalent interaction analysis unveils significant van der Waals and attractive non-covalent interactions between pesticides and the Ti2C substrate, shedding light on pesticide-nanomaterial complex stability.

Promotional mechanism of nitrogen-doping in activated carbon for formaldehyde removal: Enhanced attractive noncovalent interactions coupled with Cannizzaro-type disproportionation reaction

Inserting nitrogen (N) heteroatoms into the carbonaceous adsorbents has been confirmed to be one of efficient strategies for enhancing HCHO removal. However, the essential promotion mechanisms of specific N-containing groups (such as pyridinic-N, pyrrolic-N, and quaternary-N) remain blurred. Herein, a series of N-doped activated carbons were prepared by annealing the melamine impregnated activated carbons at 600–900 °C and used for HCHO elimination. It manifested that the HCHO elimination performance of samples was remarkably improved after N-doping and their HCHO adsorption capacities were in the order of ACN-600 (16.37 mg/g) > ACN-750 (9.87 mg/g) > ACN-900 (7.28 mg/g) > AC (5.09 mg/g). DFT calculation results revealed that there existed stronger attractive noncovalent interactions between pyrrolic-N doped carbon and HCHO due to the formation of stronger H-bonds. Therefore, the HCHO physisorption energy on pyrrolic-N doped carbon was the highest (−32.83 kJ/mol). Compared with the single physisorption mechanism of previous studies, the in-situ DRIFTS results manifested that the pyridinic-N atom (as a typical strong Lewis base) could trigger the Cannizzaro-type disproportionation reaction, which would transform toxic HCHO into relatively less toxic methanol and formic acid. Benefiting from the dual enhanced mechanisms of attractive noncovalent interactions and Cannizzaro-type disproportionation reaction, the ACN-600 manifested excellent HCHO removal performance. This study not only intrinsically discloses the promotion mechanism of specific N-containing groups on HCHO removal at molecular level but also provides guidelines for rational design and development of carbonaceous materials for effective HCHO elimination.

Erythronium Bonds: Noncovalent Interactions Involving Group 5 Elements as Electron Density Acceptors.

Analyses of the Cambridge Structural Database and theoretical calculations (PBE0-D3/def2-TZVP level, atoms-in-molecules, natural bond orbital studies) prove the formation of net attractive noncovalent interactions between group 5 elements and electron-rich atoms (neutral or anionic). These bondings are markedly different from coordination bonds formed by the same elements and possess the distinctive features of σ-hole interactions. The term erythroniumbond is proposed to denote these bonds. X-ray structures of vanadate-dependent bromoperoxidases show these interactions are present also in biological systems.

Discovery and Development of the Enantioselective Minisci Reaction.

ConspectusThe class of reactions now known as Minisci reactions is broadly defined as the addition of nucleophilic carbon-based radicals to basic heteroarenes with subsequent rearomatization to form a new carbon-carbon bond. Since the pioneering work of Minisci in the 1960s and 1970s, these reactions are now widely used in medicinal chemistry due to the ubiquity of basic heterocycles in druglike molecules. One of the long-standing challenges of Minisci chemistry has been that of regioselectivity due to the mixtures of positional isomers commonly obtained on many substrates if there is a choice between similarly activated sites. At the outset of the work described herein, we hypothesized that it may be possible to tackle this using a catalytic strategy whereby a bifunctional Brønsted acid catalyst simultaneously activates the heteroarene and engages attractive non-covalent interactions with the incoming nucleophile, resulting in a proximal attack. Using chiral BINOL-derived phosphoric acids, we not only were able to achieve this goal of regiocontrol but also discovered that we could control the absolute stereochemistry at the new stereocenter formed when prochiral α-amino radicals were employed. At the time, this discovery was unprecedented in the context of Minisci reactions.This Account details the discovery of this protocol and the further development, expansion, and investigations into the mechanism that we have carried out since then, several in collaboration with other research groups. Collaborative efforts have involved an expansion of the scope to diazines guided by multivariate statistical analysis through the development of a predictive model (collaboration with Sigman). Also, a mechanistic study involving detailed DFT analysis (collaboration with Goodman and Ermanis) unveiled the selectivity-determining step as being the deprotonation of a key cationic radical intermediate by the associated chiral phosphate anion. We have additionally carried out a number of synthetic developments of the protocol such as removing the need to prefunctionalize the radical nucleophile; hydrogen-atom transfer can be used to enable a formal coupling of two C-H bonds to form a C-C bond while retaining high enantio- and regioselectivity. Most recently, we have been able to expand the protocol so that α-hydroxy radicals can be used: until this point, all examples had concerned α-amino radicals. Again, HAT was used to generate the α-hydroxy radicals, and DFT studies carried out in collaboration (Ermanis) provided mechanistic insights.Since our original report, there have appeared a number of exciting developments from other research groups whereby the protocol has been applied to new substrates or using different precursors to generate the requisite α-amino radical. There have also been several examples in which alternative photocatalyst systems have been used to reduce the redox-active esters in the original enantioselective Minisci protocol. While primarily an Account, these contributions from other research groups will be covered briefly for context toward the end of the article.

Additive-Free Transfer Hydrogenative Direct Asymmetric Reductive Amination Using a Chiral Pyridine-Derived Half-Sandwich Catalyst.

Chiral amines are broadly used compounds in pharmaceutical industry and organic synthesis, and reductive amination reactions have been the most appreciated methods for their syntheses. However, one-step transfer hydrogenative direct asymmetric reductive amination (THDARA) that could expand the scope, simplify the operation and eliminate the use of additives has been challenging. In this work, based on the Xiao's racemic transfer hydrogenative reductive amination in 2010 and our recent work in novel chiral pyridine ligands, chiral half-sandwich iridium catalysts were rationally designed and synthesized. Using the optimized catalyst and azeotropic mixture of formic acid and triethylamine as the hydrogen source, a broad range of α-chiral (hetero)aryl amines, including various polar functional groups and heterocycles, were prepared in generally high yield and enantioselectivity under mild and operationally simple conditions. Density functional theory (DFT) calculation of the catalytically active Ir-H species and the key hydride transfer step supported the chiral pyridine-induced stereospecific generation of the iridium center, and the enantioselection by taming the highly flexible key transition structure with multiple attractive non-covalent interactions. This work introduced a type of effective chiral catalysts for simplified approach to medicinally important chiral amines, as well as a rare example of robust enantioselective transition-metal catalysis.

Enantioselective Catalysis with Pyrrolidinyl Gold(I) Complexes: DFT and NEST Analysis of the Chiral Binding Pocket.

A new generation of chiral gold(I) catalysts based on variations of complexes with JohnPhos-type ligands with a remote C2-symmetric 2,5-diarylpyrrolidine have been synthesized with different substitutions at the top and bottom aryl rings: from replacing the phosphine by a N-heterocyclic carbene (NHC) to increasing the steric hindrance with bis- or tris-biphenylphosphine scaffolds, or by directly attaching the C2-chiral pyrrolidine in the ortho-position of the dialkylphenyl phosphine. The new chiral gold(I) catalysts have been tested in the intramolecular [4+2] cycloaddition of arylalkynes with alkenes and in the atroposelective synthesis of 2-arylindoles. Interestingly, simpler catalysts with the C2-chiral pyrrolidine in the ortho-position of the dialkylphenyl phosphine led to the formation of opposite enantiomers. The chiral binding pockets of the new catalysts have been analyzed by DFT calculations. As revealed by non-covalent interaction plots, attractive non-covalent interactions between substrates and catalysts direct specific enantioselective folding. Furthermore, we have introduced the open-source tool NEST, specifically designed to account for steric effects in cylindrical-shaped complexes, which allows predicting experimental enantioselectivities in our systems.

Accurate Interaction Energies of CO2 with the 20 Naturally Occurring Amino Acids.

We have performed a series of highly accurate calculations between CO2 and the 20 naturally occurring amino acids for the investigation of the attractive noncovalent interactions. Different nucleophilic groups present in the amino acid structures are considered (α-NH2, COOH, side groups), and the stronger binding sites were identified. A database of accurate reference interactions energies was compiled as computed by explicitly-correlated coupled-cluster singles-and-doubles, together with perturbative triples extrapolated to the complete-basis-set limit. The CCSD(F12)(T)/CBS reference values were used for comparing a variety of popular density functionals with different basis sets. Our results show that most density functionals with the triple-zeta basis set def2-TZVPP align with the CCSD(F12)(T)/CBS reference values, but errors range from 0.1 kcal/mol up to 1.0 kcal/mol.

Substrate-Directed Enantioselective Aziridination of Alkenyl Alcohols Controlled by a Chiral Cation.

Alkene aziridination is a highly versatile transformation for the construction of chiral nitrogen-containing compounds. Inspired by the success of analogous substrate-directed epoxidations, we report an enantioselective aziridination of alkenyl alcohols, which enables asymmetric nitrene transfer to alkenes with varied substitution patterns, including those not covered by the current protocols. We believe that our method is effective because it is substrate-directed, exploiting a network of attractive non-covalent interactions between the substrate, an achiral dianionic rhodium(II,II) tetracarboxylate dimer, and its two associated cinchona alkaloid-derived cations. It is these cations that provide a defined chiral pocket in which the aziridination can occur. In addition to a thorough evaluation of compatible alkene classes, we advance a practical mnemonic to predict reaction outcome and disclose a range of post-functionalization protocols that highlight the unique synthetic potential of the enantioenriched aziridine-alcohol products.

Catalyst-Substrate Helical Character Matching Determines the Enantioselectivity in the Ishihara-Type Iodoarenes Catalyzed Asymmetric Kita-Dearomative Spirolactonization.

Catalyst design has traditionally focused on rigid structural elements to prevent conformational flexibility. Ishihara's elegant design of conformationally flexible C2-symmetric iodoarenes, a new class of privileged organocatalysts, for the catalytic asymmetric dearomatization (CADA) of naphthols is a notable exception. Despite the widespread use of the Ishihara catalysts for CADAs, the reaction mechanism remains the subject of debate, and the mode of asymmetric induction has not been well established. Here, we report an in-depth computational investigation of three possible mechanisms in the literature. Our results, however, reveal that this reaction is best rationalized by a fourth mechanism called "proton-transfer-coupled-dearomatization (PTCD)", which is predicted to be strongly favored over other competing pathways. The PTCD mechanism is consistent with a control experiment and further validated by applying it to rationalize the enantioselectivities. Oxidation of the flexible I(I) catalyst to catalytic active I(III) species induces a defined C2-symmetric helical chiral environment with a delicate balance between flexibility and rigidity. A match/mismatch effect between the active catalyst and the substrate's helical shape in the dearomatization transition states was observed. The helical shape match allows the active catalyst to adapt its conformation to maximize attractive noncovalent interactions, including I(III)···O halogen bond, N-H···O hydrogen bond, and π···π stacking, to stabilize the favored transition state. A stereochemical model capable of rationalizing the effect of catalyst structural variation on the enantioselectivities is developed. The present study enriches our understanding of how flexible catalysts achieve high stereoinduction and may serve as an inspiration for the future exploration of conformational flexibility for new catalyst designs.

Selenoxides as Excellent Chalcogen Bond Donors: Effect of Metal Coordination.

The chalcogen bond has been recently defined by the IUPAC as the attractive noncovalent interaction between any element of group 16 acting as an electrophile and any atom (or group of atoms) acting as a nucleophile. Commonly used chalcogen bond donor molecules are divalent selenium and tellurium derivatives that exhibit two σ-holes. In fact, the presence of two σ-hole confers to the chalcogen bonding additional possibilities with respect to the halogen bond, the most abundant σ-hole interaction. In this manuscript, we demonstrate that selenoxides are good candidates to be used as σ-hole donor molecules. Such molecules have not been analyzed before as chalcogen bond donors, as far as our knowledge extends. The σ-hole opposite to the Se=O bond is adequate for establishing strong and directional ChBs, as demonstrated herein using the Cambridge structural database (CSD) and density functional theory (DFT) calculations. Moreover, the effect of the metal coordination of the selenoxide to transition metals on the strength of the ChB interaction has been analyzed theoretically. The existence of the ChBs has been further supported by the quantum theory of atoms in molecules (QTAIM) and the noncovalent interaction plot (NCIPlot).

Circularly polarized luminescence in molecular recognition systems: Recent achievements.

Circularly polarized luminescence (CPL) dyes are recognized to be new generation materials and have been actively developed. Molecular recognition systems provide nice approaches to novel CPL materials, such as stimuli-responsive switches and chemical sensing materials. CPL may be induced simply by mixing chiral or achiral, luminescent or nonluminescent host and guest; there are several combinations. Molecular recognition can potentially save time and effort to construct well-ordered chiral structures with noncovalent attractive interactions as compared with the multi-step synthesis of covalently bonded dyes. It is a challenging subject to engage molecular recognition events with CPL, and it is important and interesting to see how it is achieved. In fact, simple molecular recognition systems can even enable the fine adjustment of CPL performance and detailed conformational/configurational analysis ofthe excited state. Here we overview the recent achievements of simple host-guest complexes capable of exhibiting CPL, summarizing concisely the host/guest structures, CPL intensities, and characteristics.

Enantioselective Giese Additions of Prochiral α-Amino Radicals.

Amines featuring an adjacent stereocenter are important building blocks, and recent years have seen remarkable growth in methods forming these via prochiral α-amino radical intermediates. However, very few can exert control over the newly formed stereocenter. We disclose a strategy to overcome this in the context of one of the most widely used radical carbon-carbon bond forming reactions, the Giese reaction. Incorporation of a removable basic heteroarene into the substrate enables a network of attractive noncovalent interactions between a phosphoric acid catalyst, the subsequently formed α-amino radical, and the Giese acceptor, allowing the catalyst to exert control during the C-C bond forming step. Deprotection of the products leads to analogues of γ-aminobutyric acid. We anticipate that this strategy will be applicable to other asymmetric radical transformations in which catalyst control is presently challenging.

Exploring Structure-Function Relationships of Aryl Pyrrolidine-Based Hydrogen-Bond Donors in Asymmetric Catalysis Using Data-Driven Techniques.

Hydrogen bond-based organocatalysts rely on networks of attractive noncovalent interactions (NCIs) to impart enantioselectivity. As a specific example, aryl pyrrolidine substituted urea, thiourea, and squaramide organocatalysts function cooperatively through hydrogen bonding and difficult-to-predict NCIs as a function of the reaction partners. To uncover the synergistic effect of the structural components of this catalyst class, we applied data science tools to study various model reactions using a derivatized, aryl pyrrolidine-based, hydrogen-bond donor (HBD) catalyst library. Through a combination of experimentally collected data and data mined from previous reports, statistical models were constructed, illuminating the general features necessary for high enantioselectivity. A distinct dependence on the identity of the electrophilic reaction partner and HBD catalyst is observed, suggesting that a general interaction is conserved throughout the reactions analyzed. The resulting models also demonstrate predictive capability by the successful improvement of a previously reported reaction using out-of-sample reaction components. Overall, this study highlights the power of data science in exploring mechanistic hypotheses in asymmetric HBD catalysis and provides a prediction platform applicable in future reaction optimization.

Noncovalent Stabilization of Radical Intermediates in the Enantioselective Hydroamination of Alkenes with Sulfonamides.

Noncovalent interactions (NCIs) are critical elements of molecular recognition in a wide variety of chemical contexts. While NCIs have been studied extensively for closed-shell molecules and ions, very little is understood about the structures and properties of NCIs involving free radical intermediates. In this report, we describe a detailed mechanistic study of the enantioselective radical hydroamination of alkenes with sulfonamides and present evidence suggesting that the basis for asymmetric induction in this process arises from attractive NCIs between a neutral sulfonamidyl radical intermediate and a chiral phosphoric acid (CPA). We describe experimental, computational, and data science-based evidence that identifies the specific radical NCIs that form the basis for the enantioselectivity. Kinetic studies support that C-N bond formation determines the enantioselectivity. Density functional theory investigations revealed the importance of both strong H-bonding between the CPA and the N-centered radical and a network of aryl-based NCIs that serve to stabilize the favored diastereomeric transition state. The contributions of these specific aryl-based NCIs to the selectivity were further confirmed through multivariate linear regression analysis by comparing the measured enantioselectivity to computed descriptors. These results highlight the power of NCIs to enable high levels of enantioselectivity in reactions involving uncharged open-shell intermediates and expand our understanding of radical-molecule interactions.

Matere Bonds vs. Multivalent Halogen and Chalcogen Bonds: Three Case Studies.

The term matere bond has been recently used to refer to an attractive noncovalent interaction between any element of group 7 acting as an electrophile and any atom (or group of atoms) acting as a nucleophile. The utilization of metals such as σ-hole donors is starting to attract the attention of the scientific community. In this manuscript, a comparison between matere bonds and well-known σ-hole interactions (halogen and chalcogen bonds) is carried out using three X-ray structures, retrieved from the Cambridge structural database (CSD), and density functional theory calculations (DFT). The novelty of this work resides in the utilization of a neutral Re(VII) system as the matere bond donor and multivalent chalcogen and halogen donors. In fact, as far as our knowledge extends, the description of σ-hole interactions in Se(VI) is unprecedented in the literature. The σ-hole interactions in Re(VII), Se(VI) and Cl(VII) electron acceptors are analyzed and compared using several computational tools.

An Enantioselective Suzuki-Miyaura Coupling To Form Axially Chiral Biphenols.

Axial chirality features prominently in molecules of biological interest as well as chiral catalyst designs, and atropisomeric 2,2'-biphenols are particularly prevalent. Atroposelective metal-catalyzed cross-coupling is an attractive and modular approach to access enantioenriched biphenols, and yet existing protocols cannot achieve this directly. We address this challenge through the use of enantiopure, sulfonated SPhos (sSPhos), an existing ligand that has until now been used only in racemic form and that derives its chirality from an atropisomeric axis that is introduced through sulfonation. We believe that attractive noncovalent interactions involving the ligand sulfonate group are responsible for the high levels of asymmetric induction that we obtain in the 2,2'-biphenol products of Suzuki-Miyaura coupling, and we have developed a highly practical resolution of sSPhos via diastereomeric salt recrystallization.