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Absolute configuration

In stereochemistry, absolute configuration refers to the precise three-dimensional spatial arrangement of atoms around a stereogenic center in a chiral molecule, which is unambiguously designated as R (rectus) or S (sinister) using the Cahn–Ingold–Prelog (CIP) priority rules.^[1] This notation specifies the handedness of the chiral center, enabling the distinction between enantiomers—non-superimposable mirror-image isomers that may exhibit identical physical properties but differ in optical rotation and biological interactions.^[2] The CIP rules, formalized in 1966, assign priorities to the four substituents attached to the stereocenter based on atomic number (with higher numbers receiving higher priority), followed by rules for ties involving multiple bonds or isotopes; the molecule is then oriented with the lowest-priority group pointing away from the observer, and the configuration is determined by whether the sequence of decreasing priorities traces a clockwise (R) or counterclockwise (S) path.^[2]^[3] Absolute configuration contrasts with relative configuration, which describes the stereochemical relationships (such as cis/trans or syn/anti) between multiple chiral centers or functional groups within a molecule without assigning specific R or S labels.^[4] Knowledge of absolute configuration is crucial for understanding the properties and functions of chiral molecules, particularly in organic synthesis, natural product chemistry, and pharmaceuticals, where enantiomers can have dramatically different pharmacological effects—for instance, one enantiomer may be therapeutic while the other is inactive or toxic.^[5]^[6] Definitive determination of absolute configuration typically relies on X-ray crystallography, which reveals atomic positions in the solid state, though complementary methods include nuclear magnetic resonance (NMR) spectroscopy with chiral derivatizing agents and circular dichroism (CD) analysis for solution-phase studies.^[7]^[4] These techniques ensure accurate stereochemical assignment, supporting applications from drug development to biochemical research.^[7]

Fundamentals of Stereochemistry

Chirality and Enantiomers

Chirality refers to the geometric property of a molecule that makes it non-superimposable on its mirror image, much like a left hand cannot be perfectly overlaid with a right hand.^[8] This property arises in molecules lacking an improper axis of rotation, such as a plane or center of symmetry. A common example is a tetrahedral carbon atom bonded to four different substituents, creating an asymmetric center that imparts overall molecular chirality.^[9] Enantiomers are pairs of chiral molecules that exist as non-superimposable mirror images of each other. These molecules share identical connectivity and physical properties, including melting points, solubilities, and chemical reactivities in achiral environments. However, they differ in their interaction with chiral reagents or environments and exhibit opposite optical rotations when interacting with plane-polarized light.^[10]^[11] In contrast, diastereomers are stereoisomers that are not mirror images, leading to distinct physical and chemical properties that allow their separation by conventional methods. Meso compounds, which contain multiple chiral centers but possess an internal plane of symmetry, are achiral overall and superimposable on their mirror images, thus lacking enantiomers.^[12]^[13] The foundational demonstration of enantiomers occurred in 1848 when Louis Pasteur manually separated the two enantiomers of sodium ammonium tartrate using tweezers, revealing their mirror-image crystal forms and opposite optical activities.^[14]

Absolute vs Relative Configuration

Absolute configuration refers to the precise three-dimensional spatial arrangement of atoms or substituents around a stereogenic center in a molecule, providing an unambiguous description that is independent of any reference to other molecules or standards._Complete_and_Semesters_I_and_II/Map:Organic_Chemistry(Wade)/06:_Stereochemistry_at_Tetrahedral_Centers/6.10:Absolute_and_Relative_Configuration-_the_distinction) This configuration is typically denoted using the R (rectus) or S (sinister) designation in the Cahn-Ingold-Prelog (CIP) priority rules, where the assignment depends solely on the atomic connections and priorities at that specific center.^[4] In contrast, relative configuration describes the stereochemical relationship between two or more stereocenters within the same molecule or between similar molecules, without specifying the absolute handedness or exact spatial orientation of each center._Complete_and_Semesters_I_and_II/Map:Organic_Chemistry(Wade)/06:_Stereochemistry_at_Tetrahedral_Centers/6.10:Absolute_and_Relative_Configuration-_the_distinction) It focuses on comparative arrangements, such as whether substituents are on the same or opposite sides, and is often determined through chemical correlations or degradation studies rather than direct structural analysis.^[4] For a molecule with a single chiral center, such as (R)-lactic acid, the absolute configuration fully specifies the arrangement of the hydroxyl, methyl, carboxyl, and hydrogen groups around the central carbon atom._Complete_and_Semesters_I_and_II/Map:Organic_Chemistry(Wade)/06:_Stereochemistry_at_Tetrahedral_Centers/6.10:Absolute_and_Relative_Configuration-_the_distinction) This designation remains invariant regardless of the molecule's context or comparisons to others.^[4] Relative configuration is illustrated in molecules with multiple stereocenters, such as in carbohydrates where the D or L series is assigned based on the configuration at the highest-numbered chiral carbon relative to D-(+)-glyceraldehyde or L-(-)-glyceraldehyde as the standard.^[15] For instance, D-glucose belongs to the D series because its penultimate chiral carbon has the same configuration as D-glyceraldehyde, though this does not specify the absolute R or S at every center.^[15] Similarly, in compounds with adjacent chiral centers like 2,3-dibromobutane, the erythro or threo nomenclature indicates whether the similar substituents are on the same (erythro) or opposite (threo) sides in a Fischer projection, denoting their relative orientation without absolute assignment.^[16] The fundamental distinction lies in their invariance and specificity: absolute configuration provides a complete, standalone description of stereochemistry that is fixed and universally applicable, whereas relative configuration depends on a chosen reference or internal comparison and may vary with the standard used, offering relational but not definitive spatial information._Complete_and_Semesters_I_and_II/Map:Organic_Chemistry(Wade)/06:_Stereochemistry_at_Tetrahedral_Centers/6.10:Absolute_and_Relative_Configuration-_the_distinction) This contrast is essential for understanding stereoisomers, including enantiomers, which differ solely in their absolute configurations.^[4]

Historical Development

Early Observations of Optical Activity

The phenomenon of optical activity, the ability of certain substances to rotate the plane of polarized light, was first systematically investigated in the early 19th century. In 1815, French physicist Jean-Baptiste Biot discovered that not only quartz crystals but also organic liquids, such as turpentine and essential oils, and their vapors exhibited this rotation, extending the observation beyond inorganic solids to organic compounds.^[17] This finding established optical activity as a general property linked to the structure of matter, prompting further inquiries into its causes. Building on these observations, German chemist Eilhard Mitscherlich contributed a pivotal insight in 1844 while studying tartrate salts. He found that sodium ammonium tartrate and sodium ammonium paratartrate (racemic acid) possessed identical chemical compositions and crystalline forms yet differed markedly in optical behavior: the former was optically active, while the latter was inactive.^[18] This discrepancy highlighted the existence of substances with the same elemental makeup but divergent physical properties, challenging prevailing views on chemical identity and setting the stage for investigations into stereoisomerism. The breakthrough linking optical activity to molecular structure came through the work of Louis Pasteur in 1848. While examining sodium ammonium paratartrate, Pasteur noticed that its crystals exhibited hemihedral faces, appearing as non-superimposable mirror images—some with facets tilted to the right and others to the left. Using tweezers and a magnifying glass under natural light, he manually separated these enantiomorphic crystals and dissolved them separately, observing that solutions of the right-handed crystals rotated polarized light clockwise (dextrorotatory), while those of the left-handed crystals rotated it counterclockwise (levorotatory) to the same degree.^[19] This experiment demonstrated that optical inactivity in the paratartrate arose from equal mixtures of these oppositely rotating forms, providing empirical evidence for the existence of enantiomers. In a landmark 1850 lecture to the Société Chimique de Paris, Pasteur articulated the connection between these observations and molecular asymmetry, proposing that the rotatory power stemmed from an inherent dissymmetry in the arrangement of atoms within the molecule itself, rather than solely from crystalline form. Although he did not yet specify the three-dimensional atomic architecture, this hypothesis shifted the focus from macroscopic crystals to microscopic molecular handedness, laying the empirical foundation for later theories of absolute configuration.

Formulation of Modern Rules

The development of modern rules for absolute configuration addressed the limitations of earlier relative nomenclature systems, such as Emil Fischer's projections, which described stereochemical relationships within series of compounds like sugars but could not specify the actual three-dimensional arrangement in space without an arbitrary reference point. These systems left a critical gap: the absolute handedness of molecules remained unknown until experimental methods allowed direct determination, prompting the need for a universal, unambiguous designation that could link relative configurations to absolute ones. This evolution was driven by advances in theoretical nomenclature and crystallographic techniques during the mid-20th century, culminating in standardized rules that enabled precise stereochemical communication across chemistry.^[20] In 1951, Robert Sidney Cahn and Christopher Kelk Ingold proposed the foundational sequence rules for specifying configuration at asymmetric carbon atoms, introducing the R (rectus, right) and S (sinister, left) descriptors based on a priority ranking of substituents by atomic number and other criteria. This system, initially applied to quadricovalent centers, provided a method to assign absolute configuration without relying on optical rotation or relative comparisons, marking a shift toward rigorous, non-arbitrary nomenclature. The rules were detailed in their seminal paper, which laid the groundwork for broader application to organic stereoisomers.^[20] A pivotal experimental confirmation came in 1951 when Johannes Martin Bijvoet, along with A. F. Peerdeman and A. J. van Bommel, used anomalous X-ray dispersion to determine the absolute configuration of sodium rubidium tartrate, thereby validating the Fischer convention for the D-series of sugars and establishing that D-glyceraldehyde corresponds to the (R)-configuration. This breakthrough provided the empirical anchor needed to correlate relative notations like D/L with absolute R/S designations, resolving long-standing uncertainties in stereochemistry. Bijvoet's method demonstrated that the dextrorotatory enantiomer in the tartrate series aligned with the right-handed arrangement under the new rules, influencing subsequent adoptions in carbohydrate and amino acid chemistry.^[21] The system was further refined through collaboration with Vladimir Prelog, who extended the rules to include more complex cases like axial chirality and allenes in a 1956 publication, enhancing their generality. By 1966, Cahn, Ingold, and Prelog consolidated and expanded the rules in a comprehensive review, solidifying the R/S framework as the preferred method for denoting absolute configuration in diverse molecular contexts. The International Union of Pure and Applied Chemistry (IUPAC) formally adopted the R/S system as the standard for absolute configuration nomenclature in its recommendations, with significant updates in 1996 to address extended applications such as stereogenic units beyond tetrahedral centers and improved handling of isotopic substituents. These revisions ensured the rules' adaptability to emerging areas like organometallic and supramolecular chemistry while maintaining backward compatibility with earlier formulations.^[22]^[2]^[23]

Methods of Determination

X-ray Crystallography

X-ray crystallography is the definitive method for determining the absolute configuration of chiral molecules, offering a direct three-dimensional map of atomic positions that reveals the spatial arrangement around stereocenters. Unlike relative configuration techniques, it distinguishes enantiomers by exploiting subtle violations in the symmetry of X-ray diffraction patterns. This approach relies on the Bijvoet method, which measures intensity differences in symmetry-related reflections to assign the correct handedness.^[24] The underlying principle involves anomalous dispersion, where X-rays near the absorption edge of heavy atoms—such as sulfur, chlorine, or bromine—cause a phase shift in the scattered waves due to partial absorption and re-emission by core electrons. This effect breaks Friedel's law, which otherwise equates the intensities of reflections hkl and \overline{h}\overline{k}\overline{l} for centrosymmetric structures, producing measurable Bijvoet differences that encode the absolute structure. For light-atom molecules lacking natural anomalous scatterers, co-crystallization with heavy-atom additives or tuning to specific wavelengths enhances these signals.^[25]^[24] The determination process starts with growing suitable single crystals, typically via slow evaporation or vapor diffusion, ensuring they are enantiopure or of known composition. Diffraction data are collected using a rotating-anode generator or synchrotron source, scanning a full sphere of reciprocal space to capture Bijvoet pairs, often at two wavelengths flanking the absorption edge for maximum contrast. Structure solution proceeds via direct methods or Patterson synthesis, followed by least-squares refinement in non-centrosymmetric space groups (e.g., P2₁2₁2₁). The Flack parameter x, refined alongside atomic coordinates, quantifies enantiomeric purity: x \approx 0 confirms the modeled enantiomer, x \approx 1 indicates inversion, and x \approx 0.5 suggests a racemic twin; reliability requires u(x) < 0.1. The finalized model yields the absolute configuration, interpretable via CIP rules as R or S.^[24] This technique's breakthrough came in 1951 when J. M. Bijvoet analyzed sodium rubidium (+)-tartrate tetrahydrate using copper Kα radiation, detecting anomalous scattering from the rubidium and tartrate oxygens to confirm the (2R,3R) configuration, validating Fischer's arbitrary D-series assignment and anchoring stereochemistry to an absolute scale. Today, synchrotron sources deliver tunable, high-brilliance X-rays, dramatically improving data quality for small molecules by reducing exposure times and enabling measurements on tiny or weakly scattering crystals, making absolute configuration routine in pharmaceutical and natural product research.^[24]

Spectroscopic and Computational Approaches

Spectroscopic methods provide valuable alternatives for determining absolute configuration in solution or non-crystalline states, particularly when X-ray crystallography is not feasible, serving as complementary tools that are often validated against crystallographic benchmarks.^[26] These techniques exploit the differential interactions of enantiomers with polarized light or magnetic fields in chiral environments, generating distinct spectral signatures that can be compared to known standards or predictions.^[27] Electronic circular dichroism (ECD) measures the differential absorption of left- and right-circularly polarized ultraviolet-visible light by chiral molecules, producing spectra sensitive to the absolute configuration due to electronic transitions in chromophores.^[28] For assignment, experimental ECD spectra are recorded and compared to those of reference compounds or theoretical simulations; for instance, in natural products like alkaloids, ECD has enabled unambiguous R/S designation by matching Cotton effects—characteristic positive or negative bands—to configurational models.^[26] This method is particularly effective for molecules with conjugated systems, where the sign and wavelength of excitonic couplings provide configurational insights, as demonstrated in the analysis of polyketides where ECD confirmed the (S)-configuration at key stereocenters.^[27] Vibrational circular dichroism (VCD) extends this principle to the infrared region, quantifying the differential absorption of circularly polarized light during molecular vibrations, which yields spectra highly specific to the three-dimensional arrangement of atoms.^[29] VCD is advantageous for its sensitivity to local stereochemistry, even in flexible molecules, and has been applied to determine the absolute configuration of terpenoids by comparing measured vibrational bands—such as those from C-H or C=O stretches—to simulated profiles, achieving assignments with >95% confidence for rigid structures.^[30] Unlike ECD, VCD provides band signs that are more directly tied to atomic positions, making it reliable for validating configurations in peptides and carbohydrates where multiple chiral centers complicate interpretation.^[31] Nuclear magnetic resonance (NMR) spectroscopy assigns absolute configuration by inducing diastereotopic differences in chiral environments, often using chiral solvating agents (CSAs) or chiral shift reagents that form transient complexes, leading to measurable chemical shift anisochronism between enantiomers.^[32] CSAs, such as cyclodextrins or crown ethers, encapsulate the analyte in a chiral cavity, causing enantiomer-specific shifts in proton or carbon signals; for example, in amino acid derivatives, the Δδ values (differences between enantiomer signals) correlate with (R) or (S) designation based on empirical rules derived from model compounds.^[33] Chiral lanthanide shift reagents, like Eu(hfc)3, coordinate to functional groups and amplify these differences, enabling configuration assignment in alcohols via the direction of shift dispersion in 1H NMR spectra.^[34] A cornerstone of NMR-based assignment is Mosher's method, introduced in 1973, which involves derivatization with α-methoxy-α-(trifluoromethyl)phenylacetic acid (MTPA) to form diastereomeric esters whose 1H NMR chemical shifts exhibit predictable patterns due to the anisotropic influence of the MTPA aryl and CF3 groups. In practice, the Δδ^{S-R} values (signed differences between (S)- and (R)-MTPA ester signals) follow a consistent sign pattern—negative in one sector and positive in another—for secondary alcohols, allowing conversion from relative to absolute configuration; this has been widely applied to over 10,000 natural products, confirming structures like that of (+)-ephedrine as (1R,2S).^[35] The method's reliability stems from the rigid conformational preference of the MTPA ester, though it requires careful solvent choice (e.g., CDCl3) to avoid anomalies.^[36] Computational approaches, primarily density functional theory (DFT), predict ECD and VCD spectra for candidate configurations, enabling matching to experimental data for absolute assignment without reference compounds.^[37] Using functionals like B3LYP or CAM-B3LYP with basis sets such as 6-311++G(d,p), DFT optimizes conformer populations via Boltzmann weighting and simulates chiroptical responses; for instance, in flavonoids, computed ECD spectra reproduced experimental bisignate Cotton effects, assigning the (2R,3S) configuration with root-mean-square deviations <0.1 eV.^[38] For VCD, time-dependent DFT (TD-DFT) accounts for vibrational modes, providing higher accuracy for aliphatic systems, as shown in the determination of sugar configurations where simulated band intensities matched observed signs within 10 cm^{-1}.^[29] These calculations are essential for complex molecules, integrating solvation models (e.g., PCM) to mimic solution-phase spectra and achieve configurational selectivity exceeding 99% for rigid scaffolds.^[31]

Nomenclature Conventions

Cahn-Ingold-Prelog (CIP) System

The Cahn-Ingold-Prelog (CIP) system establishes a rigorous framework for designating the absolute configuration of stereogenic units in organic molecules, primarily through R and S descriptors for tetrahedral centers, with extensions to other chiral elements. This nomenclature ensures unambiguous specification independent of molecular orientation or drawing convention.^[39] The priority assignment in the CIP system follows a hierarchical set of sequence rules. Under the first rule, the priority of substituents attached to the stereogenic atom is determined by the atomic number of the directly bonded atom, with higher atomic numbers receiving higher priority; for example, in bromo(chloro)(fluoro)methane, Br (atomic number 35) outranks Cl (17), F (9), and H (1).^[39] Ties at the first point of difference are resolved by proceeding outward along the substituent chains to compare the atomic numbers of the next atoms (second rule), represented via a digraph that branches at each atom to all attached groups ranked in decreasing order.^[39] If ties persist, including in cases involving isotopes, the substituent with the higher atomic mass receives priority (third rule).^[39] Multiple bonds are accommodated through the duplication principle, where a double-bonded atom is replicated as if singly bonded to two identical atoms, and the bond is treated as connected to phantom atoms (atomic number 0) to maintain valence; triple bonds involve triplication. This expansion ensures that, for instance, the priority of a vinyl group -CH=CH₂ exceeds that of an ethyl group -CH₂CH₃ because the =CH₂ carbon is digraph-expanded to -CH(CH)(CH), where the phantoms give it an effective higher ranking at the second sphere.^[39] For a tetrahedral stereocenter, once priorities (1 highest to 4 lowest) are assigned to the four substituents, the molecule is oriented with the lowest-priority group directed away from the observer. The configuration is then R if the decreasing sequence 1→2→3 traces a clockwise path, or S if counterclockwise; the descriptors derive from the Latin rectus (right) and sinister (left), respectively.^[39] If the lowest-priority group lies in the plane of the other three, its position is swapped with the in-plane group of interest, and the opposite descriptor is applied to the resulting orientation. The CIP rules extend to axial chirality, as in allenes with cumulative double bonds, where priorities are assigned to the two pairs of ligands at the terminal carbons of the axis; the configuration is determined by projecting along the axis and evaluating the helicity of the priority sequence, yielding P for a right-handed helix or M for left-handed, analogous to R/S.^[39] For planar chirality, such as in ansa compounds or small-ring systems, a reference plane is defined, and substituents are prioritized above and below it; the descriptor Rp or Sp is assigned based on whether the sequence from highest above to highest below to the next highest above is clockwise or counterclockwise when viewed from above.^[39] An illustrative application is the assignment for (R)-lactic acid, systematically named (2R)-2-hydroxypropanoic acid. The stereogenic carbon bears -OH, -COOH, -CH₃, and -H. Priority 1 is -OH (O, atomic number 8); priority 2 is -COOH, as its attached C expands to connections with two O (from =O and -OH) outranking the three H on -CH₃ (priority 3); -H is priority 4. Orienting -H away yields a clockwise 1→2→3 sequence, confirming the R designation.^[39]

Alternative Designation Systems

Alternative designation systems for chiral molecules have historically relied on either the direction of optical rotation or relative configurations compared to reference compounds, predating the universal Cahn-Ingold-Prelog (CIP) rules. These methods provide practical labels but lack the precision of absolute configuration assignments.^[40] One common approach uses the sign of optical rotation to designate enantiomers as (+) for dextrorotatory compounds, which rotate plane-polarized light clockwise, and (−) for levorotatory compounds, which rotate it counterclockwise. This convention, originating from early observations of optical activity in the 19th century, is measured using a polarimeter and applies broadly to chiral substances. Similarly, lowercase d and l (from Latin dexter for right and laevus for left) denote the same rotation directions, often used interchangeably with (+) and (−). However, these designations do not correlate with absolute handedness, as the rotation sign depends on wavelength, solvent, temperature, and molecular structure rather than the spatial arrangement at chiral centers; for instance, one enantiomer might be (+) at one wavelength but (−) at another.^[41]^[42] Another widely used system employs uppercase D and L to indicate relative configuration, particularly in carbohydrates and amino acids, based on analogy to glyceraldehyde in Fischer projections. Developed by Emil Fischer in the late 19th century, this method assigns D if the hydroxyl group on the penultimate carbon (farthest from the carbonyl) points to the right, and L if to the left, mirroring the reference enantiomers of glyceraldehyde. For example, naturally occurring sugars like D-glucose and amino acids like L-alanine follow this convention, facilitating comparisons within biochemical classes. The D-glyceraldehyde reference, specifically the (2R)-enantiomer, serves as the standard, but the system describes relative rather than absolute stereochemistry across unrelated molecules.^[43]^[40] These alternative systems introduce ambiguities because they are not absolute; for instance, (2S)-glyceraldehyde corresponds to the D series, showing no direct mapping to CIP R/S labels without additional correlation. In amino acids, most L-forms align with the S configuration, as in L-alanine, but exceptions arise due to substituent priorities—L-cysteine has the R configuration because sulfur's higher atomic number elevates the side chain in CIP ranking over the carboxyl group. Such discrepancies highlight the limitations of D/L and rotation-based notations, which can lead to confusion in diverse chemical contexts without reference to the unambiguous R/S standard.^[40]^[44]

Applications and Significance

In Pharmaceutical Chemistry

In pharmaceutical chemistry, the absolute configuration of chiral drugs plays a pivotal role in enantioselective synthesis, where producing a single enantiomer is essential to maximize therapeutic efficacy while minimizing adverse effects. Often, only one enantiomer exhibits the desired pharmacological activity, whereas the other may be inactive or even toxic. For instance, in ibuprofen, the (S)-enantiomer is responsible for the anti-inflammatory effects through potent inhibition of cyclooxygenase enzymes, while the (R)-enantiomer shows negligible activity at clinical concentrations.^[45] The thalidomide tragedy of the late 1950s and early 1960s exemplifies the risks of ignoring absolute configuration; the (R)-enantiomer provided sedative benefits, but the (S)-enantiomer caused severe teratogenic effects, leading to thousands of birth defects worldwide and highlighting the need for enantiopure formulations.^[46] This underscores the importance of determining and controlling absolute configuration during synthesis to ensure drug safety and potency. Regulatory agencies have established stringent requirements for chiral drugs to address these concerns. In 1992, the U.S. Food and Drug Administration (FDA) issued a policy statement mandating that developers study the pharmacology, pharmacokinetics, and toxicology of individual enantiomers for new stereoisomeric drugs, rather than relying solely on racemic mixtures.^[47] The European Medicines Agency (EMA) adopted similar guidelines, emphasizing the characterization of absolute configuration using systems like the Cahn-Ingold-Prelog (CIP) rules to assign R/S designations. An example is esomeprazole, the (S)-enantiomer of omeprazole, approved by the FDA in 2001 for gastroesophageal reflux disease; it demonstrates superior acid suppression and longer duration of action compared to the racemate due to its specific metabolic profile.^[48] These regulations ensure that single-enantiomer drugs undergo rigorous evaluation for enantiomeric purity and impurity control. Chiral switches, the conversion of racemic drugs to their enantiopure counterparts, further illustrate the significance of absolute configuration in optimizing drug performance. This strategy can enhance pharmacokinetics, such as improved bioavailability or reduced dosing frequency, while extending patent life. For esomeprazole, the switch from racemic omeprazole resulted in higher plasma exposure and better healing rates for erosive esophagitis, attributed to the (S)-enantiomer's slower metabolism.^[49] Over 50% of marketed drugs are chiral, making absolute configuration critical not only for therapeutic outcomes but also for intellectual property protection and regulatory approval, as impurities from the undesired enantiomer are treated as process-related contaminants.^[50]

In Biochemical and Natural Product Studies

In biological systems, enzymes and receptors exhibit high stereospecificity, selectively recognizing and interacting with one enantiomer over its mirror image due to the precise three-dimensional fit required for binding. This discrimination is evident in the universal use of L-amino acids in proteins, where enzymes such as aminoacyl-tRNA synthetases incorporate only the L-enantiomers during protein synthesis, rejecting D-forms that would disrupt folding and function. Similarly, nucleic acids like DNA incorporate D-sugars, such as β-D-2'-deoxyribose, which dictates the right-handed helical structure essential for genetic stability and replication; the L-enantiomer would form incompatible left-handed helices incompatible with enzymatic machinery.^[51]^[52] The absolute configuration of natural products profoundly influences their bioactivity, as only specific stereoisomers align with biological targets. For instance, natural morphine from the opium poppy possesses the (5R,6S,9R,13S,14R) configuration, enabling potent binding to μ-opioid receptors for analgesic effects, whereas its enantiomer is biologically inactive due to mismatched spatial orientation at the receptor site. This stereochemical selectivity underscores why nature produces enantiomerically pure compounds, ensuring efficacy in ecological and physiological roles.^[53]^[54] Biological homochirality, the predominance of one enantiomer across life's macromolecules, reflects an evolutionary selection process rooted in prebiotic origins. All proteins utilize L-amino acids, a uniformity that facilitates efficient enzymatic catalysis and structural integrity; this bias likely arose from prebiotic chemical amplifications, such as asymmetric autocatalysis or mineral surface interactions that favored L-forms in primordial soups. Studies suggest that early environmental asymmetries, including circularly polarized light from stars, could have initiated this enantiomeric excess, propagating through replication to define life's chiral blueprint.^[55]^[56] Research in the 1970s revealed that enantiomers of chiral compounds undergo differential metabolism due to enzyme selectivity, leading to distinct pharmacokinetic profiles. For example, studies on warfarin demonstrated that the S-enantiomer, more potent as an anticoagulant, has a shorter plasma half-life (approximately 24 hours) compared to the R-enantiomer (around 50 hours) in humans, attributed to stereoselective oxidation by hepatic cytochrome P450 enzymes. These findings highlighted how absolute configuration modulates clearance rates, influencing therapeutic outcomes and toxicity risks in biological systems.^[57]^[58] In complex natural products, methods like electronic circular dichroism (ECD) spectroscopy are employed to assign absolute configurations by comparing experimental spectra with computational predictions, aiding in elucidating stereochemistry critical for bioactivity.^[59]

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Determination of absolute configuration via vibrational circular ...
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Determination of Absolute Configuration Using Vibrational Circular ...
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Mosher ester analysis for the determination of absolute configuration ...
This protocol details the most commonly used nuclear magnetic resonance (NMR)-based method for deducing the configuration of otherwise unknown stereogenic, ...Missing: 1973 paper
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The assignment of absolute configurations by NMR of ...
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Computational methods and points for attention in absolute ...
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Determination of Absolute Configuration Using Density Functional ...
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Blue Book P-9 - IUPAC nomenclature
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Optical Rotation, Optical Activity, and Specific Rotation
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[PDF] Stereochemistry - Fischer Projections, Absolute Configuration and ...
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The significance of chirality in contemporary drug discovery-a mini ...
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This mini-review summarizes the overall mechanistic insights into the interconversion of l- and d-amino acids by the amino acid racemases.
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Enantioselectivity in Drug Pharmacokinetics and Toxicity
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Enantiomeric Natural Products: Occurrence and Biogenesis - PMC
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[PDF] From morphine to endogenous opioid peptides, e.g., endorphins
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Step‐by‐Step Towards Biological Homochirality – from Prebiotic ...
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Plasma half‐lives, plasma metabolites and anticoagulant efficacies ...
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Plasma half-lives, plasma metabolites and anticoagulant ... - PubMed
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Determination of the Absolute Configurations of Natural Products via ...
Electronic Circular Dichroism. Electronic excitation energies and rotational strengths have been calculated for conformations a of 1−4 using TDDFT at the B3LYP/ ...