Enantiomeric separation and determination of absolute stereochemistry of asymmetric molecules in drug discovery—Building chiral technology toolboxes

Rapid Enantiomeric Excess Measurements of Enantioisotopomers by Molecular Rotational Resonance Spectroscopy

Recent work in drug discovery has shown that selectively deuterated small molecules can improve the safety and efficacy for active pharmaceutical ingredients. The advantages derive from changes in metabolism resulting from the kinetic isotope effect when deuterium is substituted for a hydrogen atom at a structural position where rate limiting C-H bond breaking occurs. This application has pushed the development of precision deuteration strategies in synthetic chemistry that can install deuterium atoms with high regioselectivity and with stereocontrol. Copper-catalyzed alkene transfer hydrodeuteration chemistry has recently been shown to have high stereoselectivity for deuteration at the metabolically important benzyl C-H position. In this case, stereocontrol results in the creation of enantioisotopomers-molecules that are chiral solely by virtue of the deuterium substitution-and chiral analysis techniques are needed to assess the reaction selectivity. It was recently shown that chiral tag molecular rotational resonance (MRR) spectroscopy provides a routine way to measure the enantiomeric excess and establish the absolute configuration of enantioisotopomers. High-throughput implementations of chiral tag MRR spectroscopy are needed to support optimization of the chemical synthesis. A measurement methodology for high-throughput chiral analysis is demonstrated in this work. The high-throughput ee measurements are performed using cavity-enhanced MRR spectroscopy, which reduces measurement times and sample consumption by more than an order-of-magnitude compared to the previous enantioisotopomer analysis using a broadband MRR spectrometer. It is also shown that transitions for monitoring the enantiomers can be selected from a broadband rotational spectrum without the need for spectroscopic analysis. The general applicability of chiral tag MRR spectroscopy is illustrated by performing chiral analysis on six enantioisotopomer reaction products using a single molecule as the tag for chiral discrimination.

Chiral Recognition of Amino Acids Using CC2 Porous Organic Cages

Enantiomers have the same physical properties but different chemical properties due to the difference in the orientation of groups in space and thus Chiral discrimination is quite necessary, as an enantiomer of drug can have lethal effects. In this study, we used the CC2 cage for chiral discrimination of amino acids using density functional theory. The results indicated the physisorption of amino acids in the central cavity of the cage. Among the four selected amino acids, proline showed maximum interactions with the cage and maximum chiral discrimination energy is also observed in the case of proline that is 2.78 kcal/mol. Quantum theory of atoms in molecules and noncovalent interaction index analyses showed that the S enantiomer in each case has maximum interactions. The charge transfer between the analyte and surface is further studied through natural bond orbital analysis. It showed sensitivity of cage for both enantiomers, but a more pronounced effect is seen for S enantiomers. In frontier molecular orbital analysis, the least E_H-L gap is observed in the case of R proline with a maximum charge transfer of -0.24 e^-. Electron density difference analysis is carried out to analyze the pattern of the charge distribution. The partial density of state analysis is computed to understand the contribution of each enantiomer in overall density of the complexes. Our results show that S-CC2 porous organic cages have a good ability to differentiate between two enantiomers. S-CC2 porous organic cages efficiently differentiated the S enantiomer from the R enantiomers of selected amino acids.

Quantification of monosaccharide enantiomers using optical properties of hydrogen-bonded tryptophan

Chiral recognition between amino acids and monosaccharides in the gas phase was investigated as a model for chemical evolution in interstellar molecular clouds. Ultraviolet (UV) photodissociation spectra and product ion spectra of cold gas-phase hydrogen-bonded clusters of protonated tryptophan (Trp) and a pentose, including ribose and arabinose, were obtained using a tandem mass spectrometer equipped with an electrospray ionization source and a temperature-controlled ion trap. The relative intensity of the signal arising from the S₁-S₀ transition of protonated Trp observed at approximately 285 nm in the UV photodissociation spectrum of homochiral H⁺(d-Trp)(d-ribose) was significantly higher than that of heterochiral H⁺(l-Trp)(d-ribose), corresponding to the ππ* state of the Trp indole ring. Optical properties of Trp in the clusters induced by 285-nm photoexcitation were applied to the identification and quantification of pentose enantiomers in solution. Pentose enantiomeric excess in solution was determined from relative abundances observed in a single product ion spectrum of 285-nm photoexcited hydrogen-bonded clusters of H⁺(l-Trp) and pentose. A mixture of two pentoses could also be quantified by this method. The geometric and electronic structures of Trp enable recognition of biological molecules through hydrogen bonding.

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.

The ONIOM/PMM Model for Effective Yet Accurate Simulation of Optical and Chiroptical Spectra in Solution: Camphorquinone in Methanol as a Case Study

This paper deals with the development and first validation of a composite approach for the simulation of chiroptical spectra in solution aimed to strongly reduce the number of full QM computations without any significant accuracy loss. The approach starts from the quantum mechanical computation of reference spectra including vibrational averaging effects and taking average solvent effects into account by means of the polarizable continuum model. Next, the snapshots of classical molecular dynamics computations are clusterized and one reference configuration from each cluster is used to compute a reference spectrum. Local fluctuation effects within each cluster are then taken into account by means of the perturbed matrix model. The performance of the proposed approach is tested on the challenging case of the optical and chiroptical spectra of camphorquinone in methanol solution. Although further validations are surely needed, the results of this first study are quite promising also taking into account that agreement with experimental data is reached by just a couple of full quantum mechanical geometry optimizations and frequency computations.

Ab Initio Study of Circular Dichroism and Circularly Polarized Luminescence of Spin-Allowed and Spin-Forbidden Transitions: From Organic Ketones to Lanthanide Complexes

Complete and restricted active space self-consistent field (CAS-/RAS-SCF) wave function methods are applied for the calculation of circular dichroism (CD) and circularly polarized luminescence (CPL) of a series of molecules comprising four organic ketones, the chiral cobalt(III) complex [Co(en)₃]³⁺, and the europium(III) complex [Eu(DPA)₃]^3-. The ab initio results are in good agreement with the experimental data and previous results obtained with Kohn-Sham density functional theory in the case of the spin-allowed transitions. CD and CPL properties are calculated ab initio for the spin-forbidden transitions of both a transition metal and a lanthanide complex.

Accurate calculation of optically induced birefringences in chiral systems using efficient polarized basis sets

Using state-of-the-art ab initio methodology, we evaluate universal molecular parameters entering the expressions for various optically induced birefringences in chiral fluids. For this, we use the single and double excitation coupled cluster (CCSD) theory together with Dunning's augmented correlation consistent polarized basis sets of increasing size. As this is the first time these parameters are evaluated for chiral molecules using the CCSD approach, we choose possibly small test systems: a model asymmetric methane molecule, and (R)-fluoro-oxirane. With this choice, the convergence of the molecular parameters with the increase of the basis set size is investigated in detail. The results are compared to those obtained with the LPol-n (n = ds, dl, fs) and the ORP basis sets, and to the corresponding Density Functional Theory (DFT) counterparts. We can conclude that the DFT medium constant values are considerably far from coupled cluster, and therefore, aware of the known excellent performance of the CCSD method in the evaluation of various dynamic responses, we do not recommend the former methodology for accurate evaluation of the present properties. Regarding basis set convergence, the performace of the LPol-ds basis set is more efficient than that of the d-aug-cc-pVDZ set, and therefore, the former basis set can be a good choice when dealing with the study of larger systems.

Chiral metamaterials via Moiré stacking

Chiral metamaterials have attracted strong interest due to their versatile capabilities in spin-dependent light manipulation. Benefiting from advancements in nanofabrication and mechanistic understanding of chiroptical effects, chiral metamaterials have shown potential in a variety of applications including circular polarizers, chiral sensors, and chiroptical detectors. Recently, chiral metamaterials made by moiré stacking, superimposing two or more periodic patterns with different lattice constants or relative spatial displacement, have shown promise for chiroptical applications. The moiré chiral metamaterials (MCMs) take advantage of lattice-dependent chirality, giving cost-effective fabrication, flexible tunability, and reconfigurability superior to conventional chiral metamaterials. This feature article focuses on recent progress of MCMs. We discuss optical mechanisms, structural design, fabrication, and applications of the MCMs. We conclude with our perspectives on the future opportunities for the MCMs.

Solvent polarity effects on supramolecular chirality of a polyfluorene-thiophene copolymer

This study demonstrates the supramolecular chirality control of a conjugated polymer via solvent polarity. We designed and synthesized a chiral polyfluorene-thiophene copolymer having two different chiral side chains at the 9-position of the fluorene unit. Chiral cyclic and alkyl ethers with different polarities were selected as the chiral side chains. The sign of the circular dichroism spectra in the visible wavelength region was affected by the solvent system, resulting from the change of supramolecular structure. The estimation of the solubility parameter revealed that the solubility difference of the side chains contributed to the change of the circular dichroism sign, which was also observed in spin-coated films prepared from good solvents having different polarities.

Chiral and Molecular Recognition through Protonation between Aromatic Amino Acids and Tripeptides Probed by Collision-Activated Dissociation in the Gas Phase

Chiral and molecular recognition through protonation was investigated through the collision-activated dissociation (CAD) of protonated noncovalent complexes of aromatic amino acid enantiomers with l-alanine- and l-serine-containing tripeptides using a linear ion trap mass spectrometer. In the case of l-alanine-tripeptide (AAA), NH₃ loss was observed in the CAD of heterochiral H⁺(d-Trp)AAA, while H₂O loss was the main dissociation pathways for l-Trp, d-Phe, and l-Phe. The protonation site of heterochiral H⁺(d-Trp)AAA was the amino group of d-Trp, and the NH₃ loss occurred from H⁺(d-Trp). The H₂O loss indicated that the proton was attached to the l-alanine tripeptide in the noncovalent complexes. With the substitution of a central residue of l-alanine tripeptide to l-Ser, ASA recognized l-Phe by protonation to the amino group of l-Phe in homochiral H⁺(l-Phe)ASA. For the protonated noncovalent complexes of His enantiomers with tripeptides (AAA, SAA, ASA, and AAS), protonated His was observed in the spectra, except for those of heterochiral H⁺(d-His)SAA and H⁺(d-His)AAS, indicating that d-His did not accept protons from the SAA and AAS in the noncovalent complexes. The amino-acid sequences of the tripeptides required for the recognition of aromatic amino acids were determined by analyses of the CAD spectra.

A chiral spiroborate anion from diphenyl-l-tartramide [B{l-Tar(NHPh)2}2]−applied to some challenging resolutions

A chiral spiroborate anion [B{l-Tar(NHPh)₂}₂]⁻is effective in challenging high yield, 1-pot resolutions, as for the S-2-phenylpropylammonium salt shown.

Optically active distorted cyclic triptycenes: chiral stationary phases for HPLC

A pair of optically active triptycene derivatives ((R,R)- and (S,S)-8) with a distorted cyclic structure were synthesized via an intramolecular etherification and evaluated as a novel chiral selector for high-performance liquid chromatography. The (R,R)- and (S,S)-8-based chiral stationary phases (CSPs) were found to be particularly effective in the resolution of axially chiral biaryl compounds. The importance of the distorted cyclic structure present in 8 for chiral recognition was demonstrated by comparisons with the corresponding non-cyclic model compound ((R,R)-9), which did not display enantioselectivity in the separation of the test racemates.

We have succeeded in developing triptycene-based chiral stationary phases with a distorted cyclic structure, which can resolve a series of axially chiral compounds.

Enantiomeric Excess Determination for Monosaccharides Using Chiral Transmission to Cold Gas-Phase Tryptophan in Ultraviolet Photodissociation

Chiral transmission between monosaccharides and amino acids via photodissociation in the gas phase was examined using a tandem mass spectrometer fitted with an electrospray ionization source and a cold ion trap in order to investigate the origin of the homochirality of biomolecules in molecular clouds. Ultraviolet photodissociation mass spectra of cold gas-phase noncovalent complexes of the monosaccharide enantiomers glucose (Glc) and galactose (Gal) with protonated L-tryptophan H⁺(L-Trp) were obtained by photoexcitation of the indole ring of L-Trp. L-Trp dissociated via C_α-C_β bond cleavage when noncovalently complexed with D-Glc; however, no dissociation of L-Trp occurred in the homochiral H⁺(L-Trp)(L-Glc) noncovalent complex, where the energy absorbed by L-Trp was released through the evaporation of L-Glc. This enantioselective photodissociation of Trp was due to the transmission of chirality from Glc to Trp via photodissociation in the gas-phase noncovalent complexes, and was applied to the quantitative chiral analysis of monosaccharides. The enantiomeric excess of monosaccharides in solution could be determined by measuring the relative abundance of the two product ions in a single photodissociation mass spectrum of the cold gas-phase noncovalent complex with H⁺(L-Trp), and by referring to the linear relationships derived in this work. Graphical Abstract ᅟ.

A cellulose-based chiral fluorescent sensor for aromatic nitro compounds with central, axial and planar chirality

This is the first example of a powerful chiral fluorescent sensor applicable to a wide range of chiral compounds with central, axial and planar chirality.

Chiral stationary phases consisting of π-conjugated polymers bearing glucose-linked biphenyl units: reversible switching of resolution abilities based on a coil-to-helix transition

We have succeeded in developing a novel chiral stationary phase that can reversibly switch resolution abilities based on a coil-to-helix transition in a column.

Determination of the absolute stereostructure of a cyclic azobenzene from the crystal structure of the precursor containing a heavy element

Single crystal X-ray diffraction has been used as one of the common methods for the unambiguous determination of the absolute stereostructure of chiral molecules. However, this method is limited to molecules containing heavy atoms or to molecules with the possibility of functionalization with heavy elements or chiral internal references. Herein, we report the determination of the absolute stereostructure of the enantiomers of molecule (E)-2, which lacks the possibility of functionalization, using a reverse method, i.e., defunctionalization of its precursor of known stereostructure with bromine substitution (S-(-)-(E)-1). A reductive debromination of S-(-)-(E)-1 results in formation of one of the enantiomers of (E)-2. Using a combination of HPLC and CD spectroscopy we could safely assign the stereostructure of one of the enantiomers of (E)-2, the reduced product R-(-)-(E)-1.

Determination of the Absolute Configurations of Chiral Drugs Using Chiroptical Spectroscopy

Chiroptical spectroscopy has emerged as a promising tool for the determination of absolute configurations and predominant conformations of chiral molecules in academic laboratories. This promise has led to the adaption of chiroptical spectroscopic methods as valuable tools in chiral drug discovery research programs of the pharmaceutical industry. Most major pharmaceutical companies have invested in in-house chiroptical spectroscopy applications and reported successful outcomes. In the context of continuously increasing applications of chiroptical spectroscopy for chiral molecular structure determination, a review of recent developments and applications for chiral drugs is presented in this manuscript.

Substituent effect in theoretical ROA spectra

A correlational study of theoretical Raman Optical Activity spectra shows for the first time substituent effects on ROA intensity.

Bis(mandelato)borate: an effective, inexpensive spiroborate anion for chiral resolution

Bis(mandelato)borate [B(Man)2](-) (R- or S-) anions are simply prepared and appear widely effective for resolution of racemic cations. Three examples demonstrate their scope; the alkaloid tetrahydropalmatine (THP), 1,2-diaminopropane (1,2-dap) and the metal-organic complex [Co(phen)3](3+) are readily resolved, either by a facile one-pot procedure, or via counter-ion metathesis.

A molecular propeller effect for chiral separation and analysis

Enantiomers share nearly identical physical properties but have different chiral geometries, making their identification and separation difficult. Here we show that when exposed to a rotating electric field, the left- and right-handed chiral molecules rotate with the field and act as microscopic propellers; moreover, owing to their opposite handedness, they propel along the axis of field rotation in opposite directions. We introduce a new molecular parameter called hydrodynamic chirality to characterize the coupling of rotational motion of a chiral molecule into its translational motion and quantify the direction and velocity of such motion. We demonstrate >80% enrichment level of counterpart enantiomers in solution without using chiral selectors or circularly polarized light. We expect our results to have an impact on multiple applications in drug discovery, analytical and chiral chemistry, including determination of absolute configuration, as well as in influencing the understanding of artificial and natural molecular systems where rotational motion of the molecules is involved.

Two-photon absorption and two-photon circular dichroism of hexahelicene derivatives: a study of the effect of the nature of intramolecular charge transfer

Effect of the strength and nature of the extension of the π-electronic delocalization on TPA and TPCD of helicenes derivatives.

Systematic approach to conformational sampling for assigning absolute configuration using vibrational circular dichroism

Systematic methods that speed-up the assignment of absolute configuration using vibrational circular dichrosim (VCD) and simplify its usage will advance this technique into a robust platform technology. Applying VCD to pharmaceutically relevant compounds has been handled in an ad hoc fashion, relying on fragment analysis and technical shortcuts to reduce the computational time required. We leverage a large computational infrastructure to provide adequate conformational exploration which enables an accurate assignment of absolute configuration. We describe a systematic approach for rapid calculation of VCD/IR spectra and comparison with corresponding measured spectra and apply this approach to assign the correct stereochemistry of nine test cases. We suggest moving away from the fragment approach when making VCD assignments. In addition to enabling faster and more reliable VCD assignments of absolute configuration, the ability to rapidly explore conformational space and sample conformations of complex molecules will have applicability in other areas of drug discovery.

Substituent effect in theoretical VCD spectra

A correlational study shows for the first time a quantitative substituent effect on Vibrational Circular Dichroism intensity.

Residue Val237 is critical for the enantioselectivity of Penicillium expansum lipase

The shape of the hydrophobic tunnel leading to the active site of Penicillium expansum lipase (PEL) was redesigned by single-point mutations, in order to better understand enzyme enantioselectivity towards naproxen. A variant with a valine-to-glycine substitution at residue 237 exhibited almost no enantioselectivity (E = 1.1) compared with that (E = 104) of wild-type PEL. The function of the residue, Val237, in the hydrophobic tunnel was further analyzed by site-directed mutagenesis. For each of these variants a significant decrease of enantioselectivity (E < 7) was observed compared with that of wild-type enzyme. Further docking result showed that Val237 plays the most important role in stabilizing the correct orientation of (R)-naproxen. Overall, these results indicate that the residue Val237 is the key amino acid residue maintaining the enantioselectivity of the lipase.

Mechanism of inhibition of the GluA2 AMPA receptor channel opening by talampanel and its enantiomer: the stereochemistry of the 4-methyl group on the diazepine ring of 2,3-benzodiazepine derivatives

Stereoselectivity of 2,3-benzodiazepine compounds provides a unique way for the design of stereoisomers as more selective and more potent inhibitors as drug candidates for treatment of the neurological diseases involving excessive activity of AMPA receptors. Here we investigate a pair of enantiomers known as Talampanel and its (+) counterpart about their mechanism of inhibition and selectivity toward four AMPA receptor subunits or GluA1-4. We show that Talampanel is the eutomer with the endismic ratio being 14 for the closed-channel and 10 for the open-channel state of GluA2. Kinetic evidence supports that Talampanel is a noncompetitive inhibitor and it binds to the same site for those 2,3-benzodiazepine compounds with the C-4 methyl group on the diazepine ring. This site, which we term as the "M" site, recognizes preferentially those 2,3-benzodiazepine compounds with the C-4 methyl group being in the R configuration, as in the chemical structure of Talampanel. Given that Talampanel inhibits GluA1 and GluA2, but is virtually ineffective on the GluA3 and GluA4 AMPA receptor subunits, we hypothesize that the "M" site(s) on GluA1 and GluA2 to which Talampanel binds is different from that on GluA3 and GluA4. If the molecular properties of the AMPA receptors and Talampanel are used for selecting an inhibitor as a single drug candidate for controlling the activity of all AMPA receptors in vivo, Talampanel is not ideal. Our results further suggest that addition of longer acyl groups to the N-3 position should produce more potent 2,3-benzodiazepine inhibitors for the "M" site.

The Effect of the π-Electron Delocalization Curvature on the Two-Photon Circular Dichroism of Molecules with Axial Chirality

Herein we report on the theoretical-experimental study of the effect of curvature of the π-electron delocalization on the two-photon circular dichroism (TPCD) of a family of optically active biaryl derivatives (S-BINOL, S-VANOL, and S-VAPOL). The comparative analysis of the influence of the different transition moments to their corresponding TPCD rotatory strength reveals an enhanced contribution of the magnetic transition dipole moment on VAPOL. This effect is hereby attributed to the additional twist in the π-electron delocalization on this compound. TPCD measurements were done using the double L-scan technique in the picosecond regime. Theoretical calculations were completed using modern analytical response theory, within a time-dependent density functional theory (TD-DFT) approach, at both, B3LYP and CAM-B3LYP levels, with the aug-cc-pVDZ basis set for S-BINOL and S-VANOL, and 6-31G* for S-VAPOL. Solvent effects were included by means of the polarizable continuum model (PCM) in CH2Cl2.