Stereochemical Information Research Articles

Remote chirality transfer in low-dimensional hybrid metal halide semiconductors.

In hybrid metal halide perovskites, chiroptical properties typically arise from structural symmetry breaking by incorporating a chiral A-site organic cation within the structure, which may limit the compositional space. Here we demonstrate highly efficient remote chirality transfer where chirality is imposed on an otherwise achiral hybrid metal halide semiconductor by a proximal chiral molecule that is not interspersed as part of the structure yet leads to large circular dichroism dissymmetry factors (gCD) of up to 10-2. Density functional theory calculations reveal that the transfer of stereochemical information from the chiral proximal molecule to the inorganic framework is mediated by selective interaction with divalent metal cations. Anchoring of the chiral molecule induces a centro-asymmetric distortion, which is discernible up to four inorganic layers into the metal halide lattice. This concept is broadly applicable to low-dimensional hybrid metal halides with various dimensionalities (1D and 2D) allowing independent control of the composition and degree of chirality.

Site‐Selective Synthetic Modifications of the Cinchona Alkaloids

The natural product quinine has been known to humankind for centuries, and in that time has played a pivotal role in the treatment of malaria. Quinine, and the related cinchona alkaloids, have seen widespread contemporary use across chemical and biological disciplines, owing in part to the plethora of functional groups and stereochemical information contained within their scaffold. This review focuses on site‐selective synthetic modifications of the cinchona alkaloids. Our comparative analysis may act as a ‘user manual’ for the selective functionalisation of the cinchona alkaloids, and aims to promote consideration of remarkable and lesser‐understood aspects of cinchona chemistry.

Structure and noncovalent interaction analysis of half-sandwich chiral-at-metal organoruthenium complexes with planar and η6-arene-metal axial chirality

The preparation of organometallic compounds has provided new molecular complexity in molecular science. The stereochemistry of organometallics has long been a great challenge due to the large atom radius and more valency. Herein, eight ruthenium piano-stool shaped Ru complexes 2a-d and 3a-d with η6-planar chirality and Ru-center chirality were successfully synthesized and resolved, and the absolute configurations were determined by X-ray diffraction analysis. Racemization experiment revealed the stability differences of the Ru complexes in various solvents. Furthermore, in asymmetric unit of complex 3b, there are two conformers bearing opposite η6-arene-Ru axial chirality. In the supramolecular organization, all of the Ru complexes are stabilized by hydrogen bonding, C-H···π and Cl/I···π interactions. π···π interaction was only observed in complex 3b. The Hirshfeld surface analysis and 2D fingerprint plot show that the eight complexes have a similar contribution composed of different noncovalent interactions to the stabilization of crystal packing. Interestingly, only complex 3b has 3.5% C···C interaction. The pairwise interaction energies were calculated using CE-B3LYP energy model and further visualized by 3D-energy framework, which show that the dominant interaction for all complexes is dispersion. Theoretical energies of each conformer of complex 2a-d and 3a-d with η6-arene rotated at different angles was calculated by DFT method, and the energy barrier between the two conformations was around 2-3 kcal/mol. Halide ligand exchange experiments on complex (SRu)-1a were performed and the plausible mechanism was proposed. These results have provided new evidence for the design of molecules with specific fine stereochemical information for potential applications in medicinal and material chemistry.

X-ray circular dichroism measured by cross-polarization x-ray transient grating

Abstract Measuring natural circular dichroism in the x-ray regime to extract stereochemical information from chiral molecules in solution remains a challenge. This is primarily due to technical limitations of the existing synchrotron sources, which hinder access to measurements of local chirality by exploiting core hole electronic transitions. In response to this challenge, we propose an alternative approach: utilizing XFEL-based cross-polarization x-ray transient grating (XTG). This method provides an indirect means to measure x-ray circular dichroism (XCD). Notably, our findings reveal that the signal emerges only once the excited cores have undergone dephasing through relaxation. XTG is now routinely measured in the XUV regime and has recently been made available for hard x-rays. Free electron lasers now offer polarization controls, and XTG can be extended to various polarization states for the two pump beams, making XCD measured by XTG feasible with the current state-of-the-art technology.

Stereospecific radical coupling with a non-natural photodecarboxylase.

Photoenzymes are light-powered biocatalysts that typically rely on the excitation of cofactors or unnatural amino acids for their catalytic activities1,2. A notable natural example is the fatty acid photodecarboxylase (FAP), which uses light energy to convert aliphatic carboxylic acids to achiral hydrocarbons3. Here, we report a way to design a non-natural photodecarboxylase based on the excitation of enzyme-bound catalytic intermediates, instead of relying on cofactor excitation4. Iminium ions5, transiently generated from enals within the active site of an engineered class I aldolase6, can absorb violet light and function as single-electron oxidants. Activation of chiral carboxylic acids, followed by decarboxylation, generates two radicals that undergo stereospecific cross-coupling, yielding products with two stereocenters. Using the appropriate enantiopure chiral substrate, the desired diastereoisomeric product is selectively obtained with complete enantiocontrol. This finding underscores the active site's ability to transfer stereochemical information from the chiral radical precursor into the product, effectively addressing the longstanding problem of rapid racemization of chiral radicals. The resulting 'memory of chirality' scenario7 is a rarity in enantioselective radical chemistry.

Finding Relevant Retrosynthetic Disconnections for Stereocontrolled Reactions.

Machine learning-driven computer-aided synthesis planning (CASP) tools have become important tools for idea generation in the design of complex molecule synthesis but do not adequately address the stereochemical features of the target compounds. A novel approach to automated extraction of templates used in CASP that includes stereochemical information included in the US Patent and Trademark Office (USPTO) and an internal AstraZeneca database containing reactions from Reaxys, Pistachio, and AstraZeneca electronic lab notebooks is implemented in the freely available AiZynthFinder software. Three hundred sixty-seven templates covering reagent- and substrate-controlled as well as stereospecific reactions were extracted from the USPTO, while 20,724 templates were from the AstraZeneca database. The performance of these templates in multistep CASP is evaluated for 936 targets from the ChEMBL database and an in-house selection of 791 AZ designs. The potential and limitations are discussed for four case studies from ChEMBL and examples of FDA-approved drugs.

Symmetric Anion Mediated Dynamic Kinetic Asymmetric Knoevenagel Reaction for N-C and N-N Atropisomers Synthesis.

A symmetric anion mediated dynamic kinetic asymmetric Knoevenagel reaction was established as a general and efficient method for accessing both N-C and N-N atropisomers. The resulting highly enantio-pure pyridine-2,6(1H,3H)-diones exhibit diverse structures and functional groups. The key to excellent regio- and remote enantiocontrol could be owed to the hydrogen bond between the enolate anion and triflamide block of the organocatalyst. This connected the enolate anion and iminium cation by a chiral backbone. The mechanism investigation via control experiments, correlation analysis, and density functional theory calculations further revealed how the stereochemical information was transferred from the catalyst into the axially chiral pyridine-2,6(1H,3H)-diones. The synthetic applications also demonstrated the reaction's potential.

Symmetric Anion Mediated Dynamic Kinetic Asymmetric Knoevenagel Reaction for N−C and N−N Atropisomers Synthesis

A symmetric anion mediated dynamic kinetic asymmetric Knoevenagel reaction was established as a general and efficient method for accessing both N−C and N−N atropisomers. The resulting highly enantio‐pure pyridine‐2,6(1H,3H)‐diones exhibit diverse structures and functional groups. The key to excellent regio‐ and remote enantiocontrol could be owed to the hydrogen bond between the enolate anion and triflamide block of the organocatalyst. This connected the enolate anion and iminium cation by a chiral backbone. The mechanism investigation via control experiments, correlation analysis, and density functional theory calculations further revealed how the stereochemical information was transferred from the catalyst into the axially chiral pyridine‐2,6(1H,3H)‐diones. The synthetic applications also demonstrated the reaction's potential.

Stereoisomers Are Not Machine Learning's Best Friends.

This study addresses the challenge of accurately identifying stereoisomers in cheminformatics, which originates from our objective to apply machine learning to predict the association constant between cyclodextrin and a guest. Identifying stereoisomers is indeed crucial for machine learning applications. Current tools offer various molecular descriptors, including their textual representation as Isomeric SMILES that can distinguish stereoisomers. However, such representation is text-based and does not have a fixed size, so a conversion is needed to make it usable to machine learning approaches. Word embedding techniques can be used to solve this problem. Mol2vec, a word embedding approach for molecules, offers such a conversion. Unfortunately, it cannot distinguish between stereoisomers due to its inability to capture the spatial configuration of molecular structures. This study proposes several approaches that use word embedding techniques to handle molecular discrimination using stereochemical information on molecules or considering Isomeric SMILES notation as a text in Natural Language Processing. Our aim is to generate a distinct vector for each unique molecule, correctly identifying stereoisomer information in cheminformatics. The proposed approaches are then compared to our original machine learning task: predicting the association constant between cyclodextrin and a guest molecule.

Chirality Sensing in Coordination-driven Supramolecular Assemblies

Abstract: Chirality is a widespread structural characteristic found in nature and plays a vital role in the structure and functioning of almost all biological systems. Nevertheless, the translation of chirality into synthetic systems is highly intricate yet captivating, as it not only applies fundamental understanding but also has the potential to tackle significant difficulties in biochemistry and medicine. Structurally, the process of coordination-driven selfassembly involves the organization of basic molecular components into well-defined porous homochiral metal-organic cages (MOCs). This allows for a systematic investigation of the enantioselective processes occurring within the nanocavities, which have limited space and specific chiral microenvironments. This article aims to provide a comprehensive summary of the recent advancements in supramolecular chirality generated in the fascinating class of porous MOCs. It will cover the synthesis and characterization of these materials, as well as the implications of their stereochemical information in terms of chiral recognition and enantio-separation. Subsequently, a subjective viewpoint will be presented regarding the potential, possibilities, and significant challenges in the future advancement of this domain, aiming to expand the progress in creating novel chiral functional materials in the realm of chemistry and beyond.

Stereoretentive enantioconvergent reactions

Enantioconvergent reactions are pre-eminent in contemporary asymmetric synthesis as they convert both enantiomers of a racemic starting material into a single enantioenriched product, thus avoiding the maximum 50% yield associated with resolutions. All currently known enantioconvergent processes necessitate the loss or partial loss of the racemic substrate’s stereochemical information, thus limiting the potential substrate scope to molecules that contain labile stereogenic units. Here we present an alternative approach to enantioconvergent reactions that can proceed with full retention of the racemic substrate’s configuration. This uniquely stereo-economic approach is possible if the two enantiomers of a racemic starting material are joined together to form one enantiomer of a non-meso product. Experimental validation of this concept is presented using two distinct strategies: (1) a direct asymmetric coupling approach, and (2) a multicomponent approach, which exhibits statistical amplification of enantiopurity. Thus, the established dogma that enantioconvergent reactions require substrates that contain labile stereogenic units is shown to be incorrect.

Ruppert‐Prakash Reagent (TMSCF3)‐Catalyzed Chemoselective Esterification of Weinreb Amides

AbstractA straightforward TMSCF3‐catalyzed conversion of Weinreb amides into esters through the treatment with sodium alkoxides is reported. The procedure documents a genuine selectivity for the esterification of primary alcohols with Weinreb amides featuring diverse substitution pattern. The constitutive N‐methoxy fragment of these acylating agents is responsible for the unique reactivity they display, thus enabling to explore alkoxides as competent nucleophilic elements. The protocol is compatible with the fully transfer of stereochemical information embodied in the starting material, as well as, guarantees the preparation of pharmaceuticals. Mechanistic investigations revealed that under the adopted reaction conditions (NaOR, R primary) TMSCF3 does not release the trifluoromethyl (CF3−) anion – as occurs with tertiary alkoxides – but rather it catalytically activates the amidic bond.

Electrochemical Dearomatizing Methoxylation of Phenols and Naphthols: Synthetic and Computational Studies.

The electrochemical oxidative dearomatizing methoxylation of phenols and naphthols was developed. It provides an alternative route for the preparation of methoxycyclohexadienones, important and versatile synthetic intermediates, that eliminates the need for stoichiometric high-energy chemical oxidants and generates hydrogen as a sole by-product. The reaction proceeds in a simple constant current mode, in an undivided cell, and it employs standardized instrumentation. A collection of methoxycyclohexadienones derived from various 2,4,6-tri-substituted phenols and 1-substituted-2-naphthols was obtained in moderate to excellent yields. These include a complex derivative of estrone, as well as methoxylated dearomatized 1,1'-bi-2-naphthols (BINOLs). The mechanism of the reaction was subject to profound investigations using density functional theory calculations. In particular, the reactivity of two key intermediates, phenoxyl radical and phenoxenium ion, was carefully examined. The obtained results shed light on the pathway leading to the desired product and rationalize experimentally observed selectivities regarding a side benzylic methoxylation and the preference for the functionalization at the para over the ortho position. They also uncover the structure-selectivity relationship, inversely correlating the steric bulk of the substrate with its propensity to undergo the side-reaction. Moreover, the loss of stereochemical information from enantiopure BINOL substrates during the reaction is rationalized by the computations.

Enantioselective synthesis of [4]helicenes by organocatalyzed intermolecular C-H amination

Catalytic asymmetric synthesis of helically chiral molecules has remained an outstanding challenge and witnessed fairly limited progress in the past decades. Current methods to construct such compounds almost entirely rely on catalytic enantiocontrolled fused-ring system extension. Herein, we report a direct terminal peri-functionalization strategy, which allows for efficient assembling of 1,12-disubstituted [4]carbohelicenes via an organocatalyzed enantioselective amination reaction of 2-hydroxybenzo[c]phenanthrene derivates with diazodicarboxamides. The key feature of this approach is that the stereochemical information of the catalyst could be transferred into not only the helix sense but also the remote C-N axial chirality of the products, thus enabling the synthesis of [4]- and [5]helicenes with both structural diversity and stereochemical complexity in good efficiency and excellent enantiocontrol. Besides, the large-scale preparations and representative transformations of the helical products further demonstrate the practicality of this protocol. Moreover, DFT calculations reveal that both the hydrogen bonds and the C-H---π interactions between the substrates and catalyst contribute to the ideal stereochemical control.

Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly Polarized Light.

Control over the stereochemistry of metal-organic cages can give rise to useful functions that are entwined with chirality, such as stereoselective guest binding and chiroptical applications. Here, we report a chiral CuI12L4 pseudo-octahedral cage that self-assembled from condensation of triaminotriptycene, aminoquinaldine, and diformylpyridine subcomponents around CuI templates. The corners of this cage consist of six head-to-tail dicopper(I) helicates whose helical chirality can be controlled by the addition of enantiopure 1,1'-bi-2-naphthol (BINOL) during the assembly process. Chiroptical and nuclear magnetic resonance (NMR) studies elucidated the process and mechanism of stereochemical information transfer from BINOL to the cage during the assembly process. Initially formed CuI(BINOL)2 thus underwent stereoselective ligand exchange during the formation of the chiral helicate corners of the cage, which determined the overall cage stereochemistry. The resulting dicopper(I) helicate corners of the cage were also shown to generate circularly polarized luminescence.

A Powerful P-N Connection: Preparative Approaches, Reactivity, and Applications of P-Stereogenic Aminophosphines.

For more than five decades, P-stereogenic aminophosphine chalcogenides and boranes have attracted scientific attention and are still in the focus of ongoing research. In the last years, novel transition metal-based synthesis methods have been discovered, in addition to the long-known use of chiral auxiliaries. Enantiomerically pure compounds with N-P+-X- (X=O, S, BH3) motifs served as valuable reactive building blocks to provide new classes of organophosphorus derivatives, thereby preserving the stereochemical information at the phosphorus atom. Over the years, intriguing applications in organocatalysis and transition metal catalysis have been reported for some representatives. Asymmetric reductions of C=C, C=N, and C=O double bonds were feasible with selected P-stereogenic aminophosphine oxides in the presence of hydrogen transfer reagents. P-stereogenic aminophosphine boranes could be easily deprotected and used as ligands for various transition metals to enable catalytic asymmetric hydrogenations of olefins and imines. This review traces the emergence of a synthetically and catalytically powerful functional compound class with phosphorus-centered chirality in its main lines, starting from classical approaches to modern synthesis methods to current applications.

Site‐Selective C(sp3)−H Borylation of 3‐Azabicyclo[3.1.0]hexanes by Cooperative Iridium/Aluminum Catalysis

AbstractFunctionalized 3‐azabicyclo[3.1.0]hexanes are highly interesting for their physiochemical and pharmacological properties. We report an unprecedented direct bridge‐head C(sp3)−H borylation by cooperative iridium/aluminum catalysis. This reaction proceeds under mild conditions in good yields with moderate to complete site selectivities. Moreover, the use of a BINOL‐based chiral aluminum catalyst renders the synthesis of enantioenriched alkylboronate products. We also disclose its synthetic utility through rapid diversifications without any loss of the stereochemical information.

Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information

In this work, we develop a method for generating targeted hit compounds by applying deep reinforcement learning and attention mechanisms to predict binding affinity against a biological target while considering stereochemical information. The novelty of this work is a deep model Predictor that can establish the relationship between chemical structures and their corresponding pIC_{50} values. We thoroughly study the effect of different molecular descriptors such as ECFP4, ECFP6, SMILES and RDKFingerprint. Also, we demonstrated the importance of attention mechanisms to capture long-range dependencies in molecular sequences. Due to the importance of stereochemical information for the binding mechanism, this information was employed both in the prediction and generation processes. To identify the most promising hits, we apply the self-adaptive multi-objective optimization strategy. Moreover, to ensure the existence of stereochemical information, we consider all the possible enumerated stereoisomers to provide the most appropriate 3D structures. We evaluated this approach against the Ubiquitin-Specific Protease 7 (USP7) by generating putative inhibitors for this target. The predictor with SMILES notations as descriptor plus bidirectional recurrent neural network using attention mechanism has the best performance. Additionally, our methodology identify the regions of the generated molecules that are important for the interaction with the receptor’s active site. Also, the obtained results demonstrate that it is possible to discover synthesizable molecules with high biological affinity for the target, containing the indication of their optimal stereochemical conformation.

Enabling Stereochemical Communication and Stimuli-Responsive Chiroptical Properties in Biphenyl-Capped Cyclodextrins.

Chiroptical materials are gaining increasing interest due to their innovative character and their applications in optoelectronics and data encryption technologies. Fully harnessing the potential of building blocks from the "chiral pool", such as native cyclodextrins (CDs), as they often lack chromophores suitable for the construction of materials with significant chiroptical properties. Here, we present the synthesis and characterization of a two-level molecular stack consisting of a point-chiral element (CD) and an axially chiral element (biphenyl), capable of effectively translating the overall stereochemical information contained in CDs into stimuli-responsive chiroptical properties. α- and β-permethylated CDs were efficiently capped with two different 2,2'-difunctionalized 1,1'-biphenyl units. In CD derivatives containing the rigid 2,2'-dihydroxy-1,1'-biphenyl cap, two intramolecular hydrogen bonds act synergistically as stereoselective actuators, enabling effective communication between the two levels and the transfer of nonchromophoric stereochemical information from the cyclic-oligosaccharide to the atropoisomeric cap. The chiroptical properties can be finely tuned by external stimuli such as temperature and solvent. The way chirality is transferred from the CD platform to the biphenyl cap was revealed thanks to crystallographic and computational analyses, together with electronic circular dichroism (ECD) studies.

Unprecedented Benzoquinone Motifs Reveal Post-Oligomerizational Modification of Proanthocyanidins.

Proanthocyanidins (PACs) are complex flavan-3-ol polymers with stunning chemical complexity due to oxygenation patterns, oxidative phenolic ring linkages, and intricate stereochemistry of their heterocycles and inter-flavan linkages. Being promising candidates for dental restorative biomaterials, trace analysis of dentin bioactive cinnamon PACs now yielded novel trimeric (1 and 2) and tetrameric (3) PACs with unprecedented o- and p-benzoquinone motifs (benzoquinonoid PACs). Challenges in structural characterization, especially their absolute configuration, prompted the development of a new synthetic-analytical approach involving comprehensive spectroscopy, including NMR with quantum mechanics-driven 1H iterative functionalized spin analysis (HifSA) plus experimental and computational electronic circular dichroism (ECD). Vital stereochemical information was garnered from synthesizing 4-(2,5-benzoquinone)flavan-3-ols and a truncated analogue of trimer 2 as ECD models. Discovery of the first natural benzoquinonoid PACs provides new evidence to the experimentally elusive PAC biosynthesis as their formation requires two oxidative post-oligomerizational modifications (POMs) that are distinct and occur downstream from both quinone-methide-driven oligomerization and A-type linkage formation. While Nature is known to achieve structural diversity of many major compound classes by POMs, this is the first indication of PACs also following this common theme.