Stereocontrolled access to thioisosteres of nucleoside di- and triphosphates

Nucleoside diphosphates and triphosphates impact nearly every aspect of biochemistry; however, the use of such compounds as tools or medicinal leads for nucleotide-dependent enzymes and receptors is hampered by their rapid in vivo metabolism. Although a successful strategy to address the instability of the monophosphate moiety in oligonucleotide therapeutics has been accomplished by their isosteric replacement with phosphorothioates, no practical methods exist to rapidly and controllably access stereopure di- and triphosphate thioisosteres of both natural and unnatural nucleosides. Here we show how a modular, reagent-based platform can enable the stereocontrolled and scalable synthesis of a library of such molecules. This operationally simple approach provides access to pure stereoisomers of nucleoside α-thiodiphosphates and α-thiotriphosphates, as well as symmetrical or unsymmetrical dinucleoside thiodiphosphates and thiotriphosphates (including RNA cap reagents). We demonstrate that ligand-receptor interactions can be dramatically influenced by P-stereochemistry, showing that such thioisosteric replacements can have profound effects on the potency and stability of lead candidates.

Assignment of the absolute configuration of molecules that are chiral by virtue of deuterium substitution using chiral tag molecular rotational resonance spectroscopy

Chiral tag molecular rotational resonance (MRR) spectroscopy is used to assign the absolute configuration of molecules that are chiral by virtue of deuterium substitution. Interest in the improved performance of deuterated active pharmaceutical ingredients has led to the development of precision deuteration reactions. These reactions often generate enantioisotopomer reaction products that pose challenges for chiral analysis. Chiral tag rotational spectroscopy uses noncovalent derivatization of the enantioisotopomer to create the diastereomers of the 1:1 molecular complexes of the analyte and a small, chiral molecule. Assignment of the absolute configuration requires high-confidence determinations of the structures of these weakly bound complexes. A general search method, CREST, is used to identify candidate geometries. Subsequent geometry optimization using dispersion corrected density functional theory gives equilibrium geometries with sufficient accuracy to identify the isomers of the chiral tag complexes produced in the pulsed jet expansion used to introduce the sample into the MRR spectrometer. Rotational constant scaling based on the fact that the diastereomers have the same equilibrium geometry gives accurate predictions allowing identification of the homochiral and heterochiral tag complexes and, therefore, assignment of absolute configuration. The method is successfully applied to three oxygenated substrates from enantioselective Cu-catalyzed alkene transfer hydrodeuteration reaction chemistry.

Synthesis of Isotopic Atropisomers Based on 12C/13C Discrimination

Quinazolin-4-one derivatives possessing an isotopic atropisomerism (isotopic N-C axial chirality) based on ortho-¹²CH₃/¹³CH₃ discrimination were prepared. The diastereomeric quinazolin-4-ones bearing an asymmetric carbon as well as an isotopic atropisomerism were clearly discriminated by ¹H and ¹³C NMR spectra and revealed to possess high rotational stability and stereochemical purity.

Asymmetric Synthesis of Isotopic Atropisomers based on ortho-CH3/CD3 Discrimination and Their Structural Properties

N-C axially chiral 3-(2-trideuteriomethyl-4,6-dimethylphenyl)-2-ethylquinazolin-4-ones and 3-(2-trideuteriomethyl-4,6-dimethylphenyl)-2-(1-phenylpropan-2-yl)quinazolin-4-ones were prepared in high enantio- and diastereomeric purities (98% ee). These quinazolinone derivatives are isotopic atropisomers based on ortho-CH₃/CD₃ discrimination and were revealed to possess a slight optical rotation and high rotational stability.

Regio- and Diastereoselective Carbometalation Reaction of Cyclopropenes

The various facets of the chemistry of cyclopropane derivatives, the smallest carbocycle, are amazingly diverse and continue to fascinate theoreticians, synthetic or structural chemists having interest in fundamental physical, medicinal chemistry, and natural product synthesis. The challenges generated by this intriguing cyclic arrangement of only three tetravalent carbons represent a wide area of the chemical spectrum. From fundamental aspects of bonding through the synthesis of highly strained molecules, the understanding of the mode of action in biological systems to the selective cleavage into acyclic substrates makes the chemistry of these small rings fascinating. Therefore, efficient routes to prepare differently polysubstituted cyclopropanes have always been of a primordial importance. In the past decade, we and others have expanded the scope of the carbometalation reaction of cyclopropenes as a broad and general method to the formation of stereodefined cyclopropane derivatives. Although cyclopropenes, with their even higher strain energy, easily undergo addition reactions of organometallic reagents, their carbometalation reactions generate new regio-, diastereo-, and enantioselectivity issues that needed to be addressed. These various stereochemical aspects accompanied our research from its origins to today, and we are proposing in this Account, a didactic overview of the different ways by which cyclopropenes can lead to the formation of polysubstituted cyclopropanes or open-products possessing several stereogenic centers as a single regio- and diastereomer.We initially launched our research campaign on the chemistry of these strained three-membered rings by the regio- and diastereoselective copper-catalyzed carbomagnesiation of enantiomerically enriched cyclopropenyl carbinols. The directing alcohol governed both the regio- and diastereoselectivity of the addition and also served as a good leaving group as it undergoes a selective 1,2-elimination reaction to provide enantioenriched alkylidenecyclopropanes in excellent yields and enantiomeric excesses. Then, we turned our attention to the regio- and stereoselective synthesis of stereodefined tri- and tetrasubstituted cyclopropanes through the diastereoselective addition to sp²- monosubstituted cyclopropenyl ester derivatives. With the aim to further expand this concept to the formation of penta- and hexa-substituted cyclopropanes as single isomer, we had first to design the preparation of the required 1,2-disubstituted cyclopropenes that would control the regioselective addition of the organometallic derivatives. The synthesis of penta- and hexa-substituted cyclopropanes was then reported for the first time as a single regio- and diastereomer. It should be noted that the in situ formed cyclopropyl-metal intermediate is configurationally stable and can be subsequently functionalized with pure retention of the configuration by addition of electrophiles. Then, the enantioselective-catalyzed carbometalation reaction of achiral cyclopropenes allowed the synthesis of several new classes of cyclopropane derivatives in high enantiomeric ratios. Finally, by combining the regio- and diastereoselective carbometalation reaction of a cyclopropene with a subsequent reaction of the resulting cyclopropylmetal species, a selective carbon-carbon bond cleavage was observed to lead to the preparation of acyclic substrates possessing several stereocenters including a quaternary carbon stereogenic center. Our original vision of using strain within an embedded double bond in a three-membered ring has provided new routes to the stereoselective synthesis of polysubstituted cyclopropanes and has been extremely successful, as it represents a current new tool for the synthesis of persubstituted cyclopropanes as a single diastereomer.

Enantioselective Synthesis of Enantioisotopomers with Quantitative Chiral Analysis by Chiral Tag Rotational Spectroscopy

Fundamental to the synthesis of enantioenriched chiral molecules is the ability to assign absolute configuration at each stereogenic center, and to determine the enantiomeric excess for each compound. While determination of enantiomeric excess and absolute configuration is often considered routine in many facets of asymmetric synthesis, the same determinations for enantioisotopomers remains a formidable challenge. Here, we report the first highly enantioselective metal‐catalyzed synthesis of enantioisotopomers that are chiral by virtue of deuterium substitution along with the first general spectroscopic technique for assignment of the absolute configuration and quantitative determination of the enantiomeric excess of isotopically chiral molecules. Chiral tag rotational spectroscopy uses noncovalent chiral derivatization, which eliminates the possibility of racemization during derivatization, to perform the chiral analysis without the need of reference samples of the enantioisotopomer.

Molecular enantiodiscrimination by NMR spectroscopy in chiral oriented systems: Concept, tools, and applications

The study of enantiodiscriminations in relation to various facets of enantiomorphism (chirality/prochirality) and/or molecular symmetry is an exciting area of modern organic chemistry and an ongoing challenge for nuclear magnetic resonance (NMR) spectroscopists who have developed many useful analytical approaches to solve stereochemical problems. Among them, the anisotropic NMR using chiral aligning solvents has provided a set of new and original tools by making accessible all intramolecular, order-dependent NMR interactions (anisotropic interactions), such as residual chemical shift anisotropy (RCSA), residual dipolar coupling (RDC), and residual quadrupolar coupling (RQC) for spin I > 1/2, while preserving high spectral resolution. The force of NMR in enantiopure, oriented solvents lies on its ability to orient differently in average on the NMR timescale enantiomers of chiral molecules and enantiotopic elements of prochiral ones, leading distinct NMR spectra or signals to be detected. In this compendium mainly written for all chemists playing with (pro)chirality, we overview various key aspects of NMR in weakly aligning chiral solvents as the lyotropic liquid crystals (LLCs), in particular those developed in France to study (pro)chiral compounds in relation with chemists needs: study of enantiopurity of mixture, stereochemistry, natural isotopic fractionation, as well as molecular conformation and configuration. Key representative examples covering the diversity of enantiomorphism concept, and the main and most recent applications illustrating the analytical potential of this NMR in polypeptide-based chiral liquid crystals (CLCs) are examined. The latest analytical strategy developed to determine in-solution conformational distribution of flexibles solutes using NMR in polypeptide-based aligned solvents is also proposed.

Directed Regioselective Carbometallation of 1,2-Dialkyl-Substituted Cyclopropenes

A regio- and diastereoselective copper-catalyzed carbomagnesiation of 1,2-dialkylated cyclopropenes is reported. The regioselectivity is controlled by a subtle tethered Lewis basic moiety. The chelating moieties allow the differentiation between two electronically tantamount organometallic intermediates. Further functionalization grants access to polysubstituted stereodefined cyclopropanes bearing up to five alkyl groups.

Detection of Isotopic Atropisomerism Based on ortho-H/D Discrimination

Racemic and optically active 3-(2-deuteriophenyl)-2-(1-phenylpropan-2-yl)quinazoline-4-thiones were prepared. The nuclear magnetic resonance spectra clearly show that they exist as a 1:1 mixture of diastereomers due to the isotopic atropisomerism based on ortho-H/D discrimination (N-C axial chirality) and a chiral carbon.

The Deuterated "Magic Methyl" Group: A Guide to Site-Selective Trideuteromethyl Incorporation and Labeling by Using CD3 Reagents

In the field of medicinal chemistry, the precise installation of a trideuteromethyl group is gaining ever-increasing attention. Site-selective incorporation of the deuterated "magic methyl" group can provide profound pharmacological benefits and can be considered an important tool for drug optimization and development. This review provides a structured overview, according to trideuteromethylation reagent, of currently established methods for site-selective trideuteromethylation of carbon atoms. In addition to CD3 , the selective introduction of CD2 H and CDH2 groups is also considered. For all methods, the corresponding mechanism and scope are discussed whenever reported. As such, this review can be a starting point for synthetic chemists to further advance trideuteromethylation methodologies. At the same time, this review aims to be a guide for medicinal chemists, offering them the available C-CD3 formation strategies for the preparation of new or modified drugs.

Breaking the Symmetry of a Meso Compound by Isotopic Substitution: Synthesis and Stereochemical Assignment of Monodeuterated cis-Perhydroazulene

We report the synthesis and absolute configuration of monodeuterated cis-perhydroazulene (d₁-1), which is a rare example of an isotopically chiral hydrocarbon whose synthesis and stereochemical analysis are known to be particularly difficult. The synthesis features nickel-boride-catalyzed deuteration that allowed formation of the diastereomerically pure cis-fused bicyclic system in d₁-1. The vibrational circular dichroism results are in excellent agreement with the computed spectrum at ωB97XD/aug-cc-pVTZ, allowing unambiguous assignment of the absolute configuration of d₁-1.

Chemical Synthesis of [2H]-Ethyl Tosylate and Exploration of Its Crypto-optically Active Character Combining Complementary Spectroscopic Tools

Small chiral molecules are excellent candidates to push the boundaries of enantiodiscrimination analytical techniques. Here is reported the synthesis of two new deuterated chiral probes, (R)- and (S)-[²H]-ethyl tosylate, obtained with high enantiomeric excesses. Due to their crypto-optically active properties, the discrimination of each enantiomer is challenging. Whereas their enantiopurity is determined by ²H NMR in chiral anisotropic media, their identification was performed by combining quantum chemical calculations and vibrational circular dichroism analysis.

Multinuclear NMR in polypeptide liquid crystals: Three fertile decades of methodological developments and analytical challenges

NMR spectroscopy of oriented samples makes accessible residual anisotropic intramolecular NMR interactions, such as chemical shift anisotropy (RCSA), dipolar coupling (RDC), and quadrupolar coupling (RQC), while preserving high spectral resolution. In addition, in a chiral aligned environment, enantiomers of chiral molecules or enantiopic elements of prochiral compounds adopt different average orientations on the NMR timescale, and hence produce distinct NMR spectra or signals. NMR spectroscopy in chiral aligned media is a powerful analytical tool, and notably provides unique information on (pro)chirality analysis, natural isotopic fractionation, stereochemistry, as well as molecular conformation and configuration. Significant progress has been made in this area over the three last decades, particularly using polypeptide-based chiral liquid crystals (CLCs) made of organic solutions of helically chiral polymers (as PBLG) in organic solvents. This review presents an overview of NMR in polymeric LCs. In particular, we describe the theoretical tools and the major NMR methods that have been developed and applied to study (pro)chiral molecules dissolved in such oriented solvents. We also discuss the representative applications illustrating the analytical potential of this original NMR tool. This overview article is dedicated to thirty years of original contributions to the development of NMR spectroscopy in polypeptide-based chiral liquid crystals.

Asymmetric Synthesis and Stereochemical Assignment of 12C/13C Isotopomers

A synthesis of chiral hydrocarbons having C₁ axis and C₃ symmetry, which owe their chirality due to asymmetrical distribution of ¹²C/¹³C isotopes, is reported. Their absolute configurations assigned using the vibrational circular dichroism technique conform with those deduced from the absolute configurations of the parent α-formyl cyclopropanes.

Absolute Configurations of Synthetic Molecular Scaffolds from Vibrational CD Spectroscopy

Vibrational circular dichroism (VCD) spectroscopy is one of the most powerful techniques for the determination of absolute configurations (AC), as it does not require any specific UV/vis chromophores, no chemical derivatization, and no growth of suitable crystals. In the past decade, it has become increasingly recognized by chemists from various fields of synthetic chemistry such as total synthesis and drug discovery as well as from developers of asymmetric catalysts. This perspective article gives an overview about the most important experimental aspects of a VCD-based AC determination and explains the theoretical analysis. The comparison of experimental and computational spectra that leads to the final conclusion about the AC of the target molecules is described. In addition, the review summarizes unique VCD studies carried out in the period 2008-2018 that focus on the determination of unknown ACs of new compounds, which were obtained in its enantiopure form either through direct asymmetric synthesis or chiral chromatography.

2 H and 13 C NMR-Based Enantiodetection Using Polyacetylene versus Polypeptide Aligning Media: Versatile and Complementary Tools for Chemists

In this work, the practical/analytical potential of an L-valine-derived polyacetylene (PLA) lyotropic liquid crystal (LLC) is examined to spectrally discriminate enantiomers (racemic mixture) or enantiotopic directions of a large collection (23) of (pro)chiral model compounds (from rigid to flexible and polar to apolar ones), thus covering various important aspects of enantiomorphism. Experimental ² H-{¹ H} (deuterated analytes and at natural abundance level) and ¹³ C-{¹ H} NMR results are discussed in terms of the difference of ² H-RQCs or ¹³ C-RCSAs and compared to those obtained in polypeptide-type LLCs (PBLG). The analysis of the NMR results provides an overview of the enantiodifferentiation capabilities of PLA and gives useful/practical hints for the chemist to select the most appropriate chiral oriented system. Astonishing NAD NMR results were obtained in the case of one of the simplest, chiral alkanes, 3-methylhexane. From a theoretical viewpoint, the data collected highlight the key molecular factors involved in orientation/discrimination processes, as a basis for optimizing computational prediction (molecular dynamics simulation), as well as designing novel helically chiral polymers as new enantiodiscriminating aligning media. In addition, a new, robust and efficient protocol to synthesize PLA and its enantiomer (PDA) on a large scale and with small polydispersities is proposed.

Enantioselective Enzymatic Naphthoyl Ring Reduction

Birch reductions of aromatic hydrocarbons by means of single-electron-transfer steps depend on alkali metals, ammonia, and cryogenic reaction conditions. In contrast, 2-naphthoyl-coenzyme A (2-NCoA) and 5,6-dihydro-2-NCoA (5,6-DHNCoA) reductases catalyze two two-electron reductions of the naphthoyl-ring system to tetrahydronaphthoyl-CoA at ambient temperature. Using a number of substrate analogues, we provide evidence for a Meisenheimer complex-analogous intermediate during 2-NCoA reduction, whereas the subsequent reduction of 5,6-dihydro-2-NCoA is suggested to proceed via an unprecedented cationic transition state. Using vibrational circular dichroism (VCD) spectroscopy, we demonstrate that both enzymatic reductions are highly stereoselective in D₂ O, providing an enantioselective pathway to products inaccessible by Birch reduction. Moreover, we demonstrate the power of VCD spectroscopy to determine the absolute configuration of isotopically engendered alicyclic stereocenters.

Assigning the absolute configuration of single aliphatic molecules by visual inspection

Deciphering absolute configuration of a single molecule by direct visual inspection is the next step in compound identification, with far-reaching implications for medicinal chemistry, pharmacology, and natural product synthesis. We demonstrate the feasibility of this approach utilizing low temperature atomic force microscopy (AFM) with a CO-functionalized tip to determine the absolute configuration and orientation of a single, adsorbed [123]tetramantane molecule, the smallest chiral diamondoid. We differentiate between single enantiomers on Cu(111) by direct visual inspection, and furthermore identify molecular dimers and molecular clusters. The experimental results are confirmed by a computational study that allowed quantification of the corresponding intermolecular interactions. The unique toolset of absolute configuration determination combined with AFM tip manipulation opens a route for studying molecular nucleation, including chirality-driven assembly or reaction mechanisms.

Direct Detection of Hardly Detectable Hidden Chirality of Hydrocarbons and Deuterated Isotopomers by a Helical Polyacetylene through Chiral Amplification and Memory

We report the first direct chirality sensing of a series of chiral hydrocarbons and isotopically chiral compounds (deuterated isotopomers), which are almost impossible to detect by conventional optical spectroscopic methods, by a stereoregular polyacetylene bearing 2,2'-biphenol-derived pendants. The polyacetylene showed a circular dichroism due to a preferred-handed helix formation in response to the hardly detectable hidden chirality of saturated tertiary or chiroptical quaternary hydrocarbons, and deuterated isotopomers. In sharp contrast to the previously reported sensory systems, the chirality detection by the polyacetylene relies on an excess one-handed helix formation induced by the chiral hydrocarbons and deuterated isotopomers via significant amplification of the chirality followed by its static memory, through which chiral information on the minute and hidden chirality can be stored as an excess of a single-handed helix memory for a long time.

Vibrational optical activity as probe for intermolecular interactions

A detailed VCD spectroscopic analysis of well-selected chiral model systems can give valuable and unprecedented insights into intermolecular interactions such as solvation or reactant–substrate binding in catalysis.

Stereoselective Formation of Fully Substituted Ketone Enolates

The application of stereochemically defined acyclic fully substituted enolates of ketones to the enantioselective synthesis of quaternary carbon stereocenters would be highly valuable. Herein, we describe an approach leading to the formation of several new stereogenic centers through a combined metalation-addition of a carbonyl-carbamoyl transfer to reveal in situ stereodefined α,α-disubstituted enolates of ketone as a single stereoisomer. This approach could produce a series of aldol and Mannich products from enol carbamate with excellent diastereomeric ratios.