Determination Of Absolute Configuration Research Articles

Stable Axially Chiral Cyclohexylidenes from Catalytic Asymmetric Knoevenagel Condensation.

Axially chiral cycloalkylidenes are interesting but less developed axially chiral molecules. Here, a bispidine-based chiral amine catalytic system was developed to promote efficiently the asymmetric Knoevenagel condensation of N-protected oxindoles and benzofuranones with 4-substituted cyclohexanones. A variety of alkylidenecycloalkanes with stable axial chirality were obtained in good yields and fairly good er (enantiomeric ratio). Based on the absolute configuration determination of product and DFT calculations, a possible mechanism of stereoselective induction was proposed.

A derivative of trihydroxynaphthalenone and a pyrone metabolite from the endophytic fungus Talaromyces purpurpgenus

A newly discovered trihydroxynaphthalenone derivative, epoxynaphthalenone (1) involving the condensation of ortho-hydroxyl groups into an epoxy structure, and a novel pyrone metabolite characterized as pyroneaceacid (2), were extracted from Talaromyces purpurpgenus, an endophytic fungus residing in Rhododendron molle. The structures of these compounds were elucidated through a comprehensive analysis of their NMR and HRESIMS data. The determination of absolute configurations was accomplished using electronic circular dichroism (ECD) calculations and CD spectra. Notably, these recently identified metabolites exhibited a moderate inhibitory activity against xanthine oxidase (XOD).

Revisiting the Absolute Configuration of Peyssonnoside A Using Vibrational Circular Dichroism Spectroscopy

Peyssonnoside A is an unusual natural product consisting of a diterpene unit and a sulfonated monosaccharide. The experimental and theoretical comparison of Optical Rotatory Dispersion (ORD) and quantitative Nuclear Magnetic Resonance (NMR) data provided strong evidence for the stereochemistry of the diterpene unit. However, predicted Vibrational Circular Dichroism (VCD) spectra of Peyssonnoside A at the B3LYP/6-311++G(2d,2p) level showed poor correlation to the corresponding experimental spectra, preventing independent absolute configuration (AC) determination from VCD analysis. New calculations using the B3PW91 functional and the 6-311G(3df,2pd) basis set suggest that we can now independently and confidently assign the AC of Peyssonnoside A through VCD analyses. The use of f-polarization functions is responsible for the current successful assignment, compared to previously failed VCD analysis. This study highlights two important points: (a) the importance of using multiple levels of theories for satisfactorily reproducing the experimental spectra and (b) for quantitative comparisons using similarity indices, it is important to consider not only the VCD spectra but also the corresponding absorption spectra.

Two New Compounds Isolated from the Itea omeiensis and Their Anti-oxidant Activities.

Two new compounds (1-2) together with ten known compounds (3-12) were isolated for the first time from the 95 % EtOH extract of aerial parts of Itea omeiensis. Their structures were elucidated based on extensive spectroscopic analyses and comparison with published data. The structure of 1 was further confirmed through single-crystal X-ray diffraction analysis, and circular dichroism (CD) spectrum in combination with acid hydrolysis was employed for the absolute configuration determination of 2. Compound 1 was the first 2-arylbenzo[b]furan with an extra six-membered lactone ring from Itea plants. Anti-oxidant assays indicated that compound 1 possessed significant radical scavenging effects on 1,1-Diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS⋅+ ) with IC50 values of 0.14 and 0.06 mg/mL, respectively, which were comparable to the positive control of ascorbic acid. However, no obvious anti-hepatocellular carcinoma activity was observed for compounds 1 and 2.

The Diterpenoid Substrate Analogue 19-nor-GGPP Reveals Pronounced Methyl Group Effects in Diterpene Cyclisations.

The substrate analogue 19-nor-geranylgeranyl diphosphate (19-nor-GGPP) was synthesised and incubated with 20 diterpene synthases, resulting in the formation of diterpenoids in all cases. A total of 23 different compounds were isolated from these enzyme reactions and structurally characterised, if possible including the experimental determination of absolute configurations through a stereoselective deuteration approach. In several cases the missing 19-Me group in the substrate analogue resulted in opening of completely new reaction paths towards compounds with novel skeletons. DFT calculations were applied to gain a deeper understanding of these observed methyl group effects in diterpene biosynthesis.

Synthesis, crystal structure, DFT calculation and confirmation of absolute configuration of empagliflozin

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by long-term disruptions in metabolism. In the course of drug development over the past decades, sodium-glucose cotransporter 2 (SGLT2) has emerged as a novel therapeutic target for treating T2DM. Empagliflozin, a significant pharmacologically active aryl glycoside, functions as a sodium-glucose cotransporter 2 (SGLT2) inhibitor and has been extensively used for blood glucose control in patients with both T2DM and diagnosed cardiovascular disease (CVD). In this study, empagliflozin was synthesized through a six-step reaction and subjected to single-crystal growth, with its structure analyzed via X-ray diffraction. Subsequently, comprehensive computational predictions of empagliflozin's structural properties were carried out using DFT theory, encompassing infrared, nuclear magnetic resonance, Raman spectra, and ECD measurements. The results were subjected to a combined analysis with experimental data, bearing significant implications for the spectral analysis and absolute configuration determination of empagliflozin. In order to gain insights into the reasons behind the formation of empagliflozin crystals, a single crystal structure analysis was performed. Additionally, DFT calculations were employed to investigate various physicochemical properties of empagliflozin, including RDG, ELF, FMOs, MEP, etc. This study aimed to provide insights into the physicochemical properties of empagliflozin and its various non-covalent interactions. The findings are anticipated to provide valuable insights for subsequent structure optimization and drug discovery endeavors.

ENANTIOSELECTIVE AND CHEMOSELECTIVE OPTICAL DETECTION OF CHIRAL ORGANIC COMPOUNDS WITHOUT RESORTING TO CHROMATOGRAPHY.

Enantiorecognition and resolution are of essential importance in many diverse areas of science. Whenever there arises a need to analyze/investigate enantiomers in different situations chromatography stands up in our minds immediately. Nevertheless, chemoselective and enantioselective recognition/discrimination (without going for separation) constitutes a different perception and requirement. The techniques using chiroptical sensing cause detection based on molecular interactions induced in different manners. Enantioselective sensing of monosaccharides in γ-cyclodextrin assembly and by diboronic acid based fluorescent sensors, application of bi-naphthol and H8BINOL based sensors and dendrimers, metal-to-ligand charge transfer transitions in CD, exciton-coupled circular dichroism, surface enhanced Raman spectroscopy, and enantioselective indicator displacement sensor arrays for enantioselective recognition/detection of chiral organic compounds, such as amines, amino acids/alcohols, and hydroxycarboxylic acids have been discussed in progressive manner with mechanistic explanations, wherever available. Besides, the chiroptical vs LC approach has been discussed. The present paper is focused on certain different non-chromatographic optical techniques and aims to extend an understanding and a view to consider such techniques which have been successful in selective detection, and determination of absolute configuration and enantiomeric excess, (without resorting to separation vis-à-vis LC) and that have potential use in high-throughput chiral assay and combinatorial search for asymmetric catalysts and reagents.

Evaluating the enantioselective capability of a cellulose tris(3,5‐dimethylphenyl carbamate)‐based stationary phase towards 5,7,2'‐trihydroxyflavanone

AbstractIn this study, an evaluation of the enantioselective of a chiral flavanone with 2'‐OH substitution (5,7,2'‐trihydroxyflavanone) on ring C was studied by high performance liquid chromatography using the cellulose tris(3,5‐dimethylphenyl carbamate)‐based stationary phase with n‐hexane and iso‐propanol doped with 0.1% (v/v) trifluoroacetic acid as a mobile phase. Column temperature and mobile phase composition were investigated in the assessment of the chiral separation by considering the enantiomeric resolution factor (Rs). Also, the absolute configurations of single enantiomers were determined by measuring CD spectra based on the exciton‐coupling method. The results pointed out that the 2'‐hydroxy group was capable of advancing the enantioselective of flavanones on the cellulose tris(3,5‐dimethylphenyl carbamate)‐based stationary phase when the column temperature was higher than 30 oC and the mobile phase was of 10% iso‐propanol doped with 0.1% (v/v) TFA in n‐hexane. The absolute configuration determination showed that the enantiomer with the 2S configuration was the first eluted and, consequently, the elution order of the enantiomers of 5,7,2'‐trihydroxyflavanone at optimal conditions was in contrast to 5,7,4'‐trihydroxyflavanone and 5,7‐dihydroxyflavanone. The 2'‐OH substitution on the phenyl moiety appears to be capable of inducing or altering the strength of inter‐and intramolecular interactions when the chiral selectors are immobilized on the silica stationary phase.

Supramolecular Chirogenesis in a Sterically Hindered Porphyrin: A Critical Theoretical Analysis.

The determination of molecular stereochemistry and absolute configuration is an important part of modern chemistry, pharmacology, and biology. Electronic circular dichroism (ECD) spectroscopy is a widely used tool for chirality assignment, especially with porphyrin macrocycles employed as reporter chromophores. However, the mechanisms of induced ECD in porphyrin complexes are yet to be comprehensively rationalized. In this work, the ECD spectra of a sterically hindered hexa-cationic porphyrin with two camphorsulfonic acids in dichloromethane and chloroform were experimentally measured and computationally analyzed. The influence of geometric factors such as the position of chiral guest molecules, distortion of the porphyrin macrocycle, and orientation of aromatic and non-aromatic peripheral substituents on the ECD spectra was theoretically studied. Various potential pitfalls, such as a lack of significant conformations and accidental agreement of experimental and simulated spectra, are considered and discussed.

Absolute configuration determination of small molecules with MicroED

Absolute configuration determination of small molecules with MicroED

Vibrational Circular Dichroism Spectroscopy of Chiral Molecular Crystals: Insights from Theory.

Chirality is a curious phenomenon that appears in various forms. While the concept of molecular (RS-)chirality is ubiquitous in chemistry, there are also more intricate forms of structural chirality. One of them is the enantiomorphism of crystals, especially molecular crystals, that describes the lack of mirror symmetry in the unit cell. Its relation to molecular chirality is not obvious, but still an open question, which can be addressed with chiroptical tools. Vibrational circular dichroism (VCD) denotes chiral infrared (IR) spectroscopy that is susceptible to both, the molecular as well as the intermolecular space by means of vibrational transitions. When carried out in the solid state, VCD delivers a very rich set of non-local contributions that are determined by crystal packing and collective motion. Since its discovery in the 1970s, VCD has become the method of choice for the determination of absolute configurations, but its applicability reaches beyond towards the study of different crystal forms and polymorphism. This brief review summarises the theoretical concepts of crystal chirality and how computations of solid-state VCD can shed light into the intimate connection of chiral structure and vibrational optical activity.

Vibrational Circular Dichroism Spectroscopy of Chiral Molecular Crystals: Insights from Theory

AbstractChirality is a curious phenomenon that appears in various forms. While the concept of molecular (RS‐)chirality is ubiquitous in chemistry, there are also more intricate forms of structural chirality. One of them is the enantiomorphism of crystals, especially molecular crystals, that describes the lack of mirror symmetry in the unit cell. Its relation to molecular chirality is not obvious, but still an open question, which can be addressed with chiroptical tools. Vibrational circular dichroism (VCD) denotes chiral infrared (IR) spectroscopy that is susceptible to both, the molecular as well as the intermolecular space by means of vibrational transitions. When carried out in the solid state, VCD delivers a very rich set of non‐local contributions that are determined by crystal packing and collective motion. Since its discovery in the 1970s, VCD has become the method of choice for the determination of absolute configurations, but its applicability reaches beyond towards the study of different crystal forms and polymorphism. This brief review summarises the theoretical concepts of crystal chirality and how computations of solid‐state VCD can shed light into the intimate connection of chiral structure and vibrational optical activity.

Enantio-resolution of some chiral sulfoxide drugs on amylose and cellulose-based stationary phases: Elution order, absolute configuration and chiral mechanism determination

The enantio-separation of three chiral sulfoxide drugs (omeprazole, pantoprazole, and lansoprazole) was achieved on Chiralpak® AS-3R column with acetonitrile‐water (65:35) at 0.5 mL/min flow and 280 nm detection within 7 min. Chiralseparation was validated properly with 9.70–14.16 and 29.39–42.91 µg.mL−1 as LOD and LOQ. The thermodynamics parameters were in the range of (-0.51 to −1,288) kJmol−1K−1(ΔG). These values confirmed chiral separation as spontaneous and thermodynamically stable. Enantiomer elution order determined on Chiralpak® IA with ethanol-hexane (95:5)at 1.0 mL/min flow at 221, 254, 270, 280,301, and 330 nm wavelengths confirmed first elution od S-enantiomer followed by R-enantiomer. This observation was also confirmed by theoretical simulations of electronic circular dichroism (ECD) calculation. The docking study was used to explain the chiral resolution of the reported drugs. As a result, a simple, fast, reliable and spontaneous and thermodynamically stable HPLC method was developed for the separation and determination of enantiomer elution order of the reported chiral sulfoxide drugs.

Total Synthesis and Absolute Configuration Determination of the α-Glycosidase Inhibitor (3S,4R)-6-Acetyl-3-hydroxy-2,2-dimethylchroman-4-yl (Z)-2-Methylbut-2-enoate from Ageratina grandifolia.

Herein, we report the first total synthesis of α-glycosidase inhibitor (3R, 4S)-6-acetyl-3-hydroxy-2,2-dimethylchroman-4-yl (Z)-2-methylbut-2-enoate as well as its enantiomer. Our synthesis confirms the chromane structure separately proposed by Navarro-Vazquez and Mata, on the basis of DFT computations. Furthermore, our synthesis allowed us to determine the absolute configuration of the natural compound as (3S, 4R) and not (3R, 4S).

Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data

Continuous-rotation 3D electron diffraction methods are increasingly popular for the structure analysis of very small organic molecular crystals and crystalline inorganic materials. Dynamical diffraction effects cause non-linear deviations from kinematical intensities that present issues in structure analysis. Here, a method for structure analysis of continuous-rotation 3D electron diffraction data is presented that takes multiple scattering effects into account. Dynamical and kinematical refinements of 12 compounds—ranging from small organic compounds to metal–organic frameworks to inorganic materials—are compared, for which the new approach yields significantly improved models in terms of accuracy and reliability with up to fourfold reduction of the noise level in difference Fourier maps. The intrinsic sensitivity of dynamical diffraction to the absolute structure is also used to assign the handedness of 58 crystals of 9 different chiral compounds, showing that 3D electron diffraction is a reliable tool for the routine determination of absolute structures.

Interpreting vibrational circular dichroism spectra: the Cai•factor for absolute configuration with confidence

Vibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs of small organic compounds and we use this database to validate a method for the automated analysis of VCD spectra and the assignment of absolute configuration: the Cai•factor (Configuration: absolute information). The analysis of the data demonstrates that the procedure is a reliable and time-efficient method for determination of absolute configuration, which gives both the assignment and a measure of confidence in the outcome, even when the spectra are imperfect. The majority of molecules tested have a high confidence score and all of these have the correct assignment.

Absolute Configuration Determination of Chiral API Molecules by MicroED Analysis of Cocrystal Powders Formed Based on Cocrystal Propensity Prediction Calculations.

Establishing the absolute configuration of chiral active pharmaceutical ingredients (APIs) is of great importance. Single crystal X-ray diffraction (scXRD) has traditionally been the method of choice for such analysis, but scXRD requires the growth of large crystals, which can be challenging. Here, we present a method for determining absolute configuration that does not rely on the growth of large crystals. By examining microcrystals formed with chiral probes (small chiral compounds such as amino acids), absolute configuration can be unambiguously determined by microcrystal electron diffraction (MicroED). Our streamlined method employs three steps: (1) virtual screening to identify promising chiral probes, (2) experimental cocrystal screening and (3) structure determination by MicroED and absolute configuration assignment. We successfully applied this method to analyze two chiral API molecules currently on the market for which scXRD was not used to determine absolute configuration.

Indazole-derived synthetic cannabinoids: Absolute configuration determination and structure characterization by circular dichroism and DFT calculations

An increasing number of products containing synthetic cannabinoids pose a growing crisis to public health worldwide. Recently, a rising number of cases of serious adverse health effects, intoxications, and death cases associated with synthetic cannabinoids were reported. The current study represents the comprehensive structural analysis of three new synthetic cannabinoids (AB-, ADB- and AMB-FUBINACA) in solution investigated by electronic and vibrational circular dichroism together with the conventional methods of infrared and ultraviolet absorption spectroscopy, all supported by the density functional theory (DFT) calculations. The best level of theory to reproduce the experimental wavenumbers and wavelengths was found to be the B3PW91 method with a 6-311++G(d,p) basis set including the implicit solvent effect simulation. Very good agreement between the experimental and simulated spectra allowed us to determine the absolute configuration and a detailed interpretation of the IR absorption, VCD, ECD and UV spectra of AB-, ADB- and AMB-FUBINACA. In addition, the HOMO and LUMO electronic transitions were calculated.

Computational methods and points for attention in absolute configuration determination

With the rapid development of high performance computers and computational methods, including software, an increasing number of experimental chemists have tried to use computational methods such as optical rotation (OR, including the matrix model), optical rotatory dispersion (ORD), electronic circular dichroism (ECD or CD), vibrational circular dichroism (VCD), and magnetic shielding constants—nuclear magnetic resonance (NMR)—to explain and/or assign absolute configuration (AC) for various compounds. Such reports in the field of natural products have increased dramatically. However, every method has its range of application. This leads, in some cases, to incorrect conclusions by researchers who are not familiar with these methods. In this review, we provide experimental chemists and researchers with more computational details and suitable suggestions, and especially hope that this experience may help readers avoid computational pitfalls. Finally, we discuss the use of simplified models to replace original complex structures with a long side chain. The fundamental basis for using models to represent complex chiral compounds, such as in OR calculations, is the existence of conformation pairs with near canceling conformer contributions that justify the use of models rather than the original compounds. Using examples, we here introduce the transition state (TS) calculation, which may benefit readers in this area for use and mastery for their AC study. This review will summarize the general concepts involved in the study of AC determinations.

Modelling solute-solvent interactions in VCD spectra analysis with the micro-solvation approach.

Vibrational circular dichroism (VCD) spectroscopy has become an important part of the (stereo-)chemists' toolbox as a reliable method for the determination of absolute configurations. Being the chiroptical version of infrared spectroscopy, it has also been recognized as being very sensitive to conformational changes and intermolecular interactions. This sensitivity originates from the fact that the VCD spectra of individual conformers are often more different than their IR spectra, so that changes in conformational distributions or band positions and intensities become more pronounced. What is an advantage for studies focussing on intermolecular interactions can, however, quickly turn into a major obstacle during AC determinations: solute-solvent interactions can have a strong influence on spectral signatures and they must be accurately treated when simulating VCD and IR spectra. In this perspective, we showcase selected examples which exhibit particularly pronounced solvent effects. It is demonstrated that it is typically sufficient to model solute-solvent interactions by placing single solvent molecules near hydrogen bonding sites of the solute and subsequently use the optimized structures for spectra simulations. This micro-solvation approach works reasonably well for medium-sized, not too conformationally flexible molecules. We thus also discuss its limitations and outline the next steps that method development needs to take in order to further improve the workflows for VCD spectra predictions.