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Epimer

An epimer is one of a pair of stereoisomers that differ in absolute configuration at only one stereogenic center, making them a specific type of diastereomer rather than enantiomers.^[1] This configuration difference arises in molecules with multiple chiral centers, where the stereochemistry at all but one center remains identical.^[2] Epimers are particularly significant in organic chemistry and biochemistry, as subtle changes in stereochemistry can profoundly influence molecular properties, reactivity, and biological activity.^[3] In the context of carbohydrates, epimers are commonly encountered among monosaccharides, where they differ in the orientation of hydroxyl groups at a single carbon atom.^[4] For instance, D-glucose and D-mannose are C2-epimers, differing at the second carbon, while D-glucose and D-galactose are C4-epimers, differing at the fourth carbon.^[2] These examples highlight how epimerization— the interconversion between epimers—plays a key role in metabolic pathways, such as the transformation of glucose to mannose in glycoprotein biosynthesis.^[5] Biologically important epimers like mannose and galactose serve distinct functions; mannose is involved in immune responses and bacterial cell walls, whereas galactose is essential for lactose synthesis and glycolipid formation.^[4] A special case of epimers occurs in cyclic carbohydrates, known as anomers, which differ specifically at the anomeric carbon (typically C1 in aldoses).^[2] For example, α-D-glucose and β-D-glucose are anomers, with the hydroxyl group at C1 oriented trans or cis to the CH₂OH group at C5 in the pyranose ring, respectively.^[2] This anomeric distinction affects stability, solubility, and enzymatic recognition, underscoring the broader implications of epimeric relationships in processes like digestion and energy storage. Beyond carbohydrates, epimers appear in pharmaceuticals and natural products, where epimerization influences drug efficacy and toxicity, as seen in tetracyclines, where the 4-epimer exhibits reduced antibiotic activity.^[6]

Definition and Terminology

Definition

An epimer is a type of stereoisomer classified as a diastereomer, characterized by having the opposite configuration at only one of two or more tetrahedral stereogenic centers, while maintaining identical configurations at all other stereogenic centers.^[7] This distinguishes epimers from other stereoisomers, as they share the same molecular connectivity and differ solely in the spatial arrangement at a single chiral site among multiple present in the molecule.^[1] Unlike enantiomers, which are nonsuperimposable mirror images differing in configuration at all chiral centers and exhibit identical physical properties except for optical rotation, epimers possess distinct physical and chemical properties due to their diastereomeric relationship.^[8]^[9] For epimers to exist, the molecule must contain at least two chiral centers, as a single chiral center would only allow for enantiomers rather than this specific subtype of diastereomer.^[10]

Relation to Stereoisomers

Epimers are a specialized category within the broader class of stereoisomers, which encompass molecules sharing identical molecular formulas and connectivity but differing in the three-dimensional arrangement of atoms. Stereoisomers are primarily classified into enantiomers—non-superimposable mirror images that differ in configuration at all chiral centers—and diastereomers, which are stereoisomers lacking such mirror-image symmetry and differing in configuration at one or more, but not all, chiral centers. Epimers specifically denote diastereomers that vary in configuration at precisely one chiral center, positioning them as a subset of diastereomers in the stereochemical hierarchy.^[11] This single-point difference distinguishes epimers from other stereoisomers, as it results in molecules with identical connectivity yet divergent spatial orientations at that stereocenter, leading to observable variations in physical and chemical properties. Unlike enantiomers, which exhibit identical NMR spectra, solubilities, and reactivities under achiral conditions, epimers display distinct NMR spectra due to their diastereomeric nature, as well as differences in reactivity influenced by the altered stereochemistry. Anomers constitute a particular subclass of epimers, arising from inversion at the anomeric carbon—the carbonyl-derived carbon in cyclic forms—highlighting how epimeric relationships can manifest in specific structural contexts.^[12]^[13]

Stereoisomer Type	Definition	Chiral Center Difference	Key Properties
Enantiomers	Non-superimposable mirror images	All chiral centers	Identical physical properties (e.g., NMR, melting point) under achiral conditions; opposite optical rotation
Diastereomers	Stereoisomers that are not mirror images	Some but not all chiral centers	Distinct physical and chemical properties (e.g., different NMR spectra, reactivity)
Epimers	Subset of diastereomers differing at one chiral center	Exactly one chiral center	Distinct properties similar to diastereomers; specific to single stereocenter inversion
Anomers	Special case of epimers at the anomeric carbon in cyclic structures	Only the anomeric carbon	Distinct properties; interconvert via ring opening in solution

This tabular overview illustrates the relational distinctions, emphasizing how epimers bridge general diastereomeric behavior with precise configurational specificity.^[11]^[14]

Structural Characteristics

Chiral Center Differences

Epimers differ from one another solely in the configuration at a single chiral center, which is typically a tetrahedral carbon atom hybridized in the sp³ state. This configuration inversion involves swapping the spatial positions of two substituents around the affected carbon, thereby altering the three-dimensional arrangement of the molecule's groups without modifying the overall skeletal structure or connectivity. Such a change results in a distinct stereoisomer that is not superimposable on its counterpart, yet shares the same molecular formula and most structural features.^[15]^[16] To visualize this difference, Fischer projections are frequently employed, particularly for acyclic representations of polyfunctional molecules like those in organic chemistry. In these projections, the differing chiral center is illustrated by interchanging the horizontal bonds (representing substituents projecting toward the viewer) at that specific carbon atom, which flips its absolute configuration from R to S or vice versa. All other vertical and horizontal bonds remain unchanged, highlighting the isolated nature of the stereochemical variation. This representational tool underscores the geometric consequence: a localized perturbation in spatial orientation that propagates subtle effects throughout the molecule's conformation.^[17] The preservation of identical configurations at all remaining chiral centers is a defining feature that sets epimers apart from enantiomers, the latter being complete mirror images that invert stereochemistry at every chiral site. This partial inversion ensures epimers are diastereomers, leading to non-identical physical properties despite their close structural similarity. For instance, epimers often exhibit variations in melting points and solubilities due to differences in crystal packing and intermolecular forces influenced by the altered geometry. Additionally, their distinct biological activities stem from differential binding affinities to chiral receptors or enzymes, as the single configuration change can significantly impact molecular recognition.^[11]^[18]^[19]

Nomenclature Conventions

The nomenclature of epimers relies on standardized prefixes to denote inversion of configuration at a single chiral center relative to a reference stereoisomer, facilitating precise identification in chemical structures. The prefix "epi-" is widely employed for this purpose, typically prefixed to the name of the parent compound and accompanied by the locant of the differing stereogenic center, such as "3-epi-" to indicate inversion at the third carbon atom.^[20] This system traces its origins to early stereochemical studies and is particularly useful in classes of compounds like alkaloids and steroids where epimeric pairs are common.^[21] IUPAC guidelines for naming epimers emphasize systematic designation, often based on the lowest numbered differing chiral carbon when selecting the parent hydride or structure to ensure the simplest name. In preferred IUPAC names, configurations are specified using R/S stereodescriptors for each stereogenic center, with the epimeric difference highlighted by contrasting the descriptor at the inverted position (e.g., (2R,3S)- versus (2S,3S)- for a C-2 epimer).^[22] This approach integrates with broader stereochemical rules in the IUPAC Blue Book (P-93), prioritizing unambiguous specification over traditional relative terms. Historically, epimer nomenclature evolved from ad hoc descriptive terms in 19th-century carbohydrate research to the formalized D/L series established by Emil Fischer around 1891, which classified sugars based on configuration at the highest-numbered asymmetric carbon relative to D- or L-glyceraldehyde.^[23] This D/L convention, refined through IUPAC commissions in the mid-20th century (e.g., 1952 and 1963 recommendations), provided a relative framework but lacked precision for multiple centers; modern practice has shifted toward locant-specific descriptors and absolute R/S notation to accommodate complex molecules in organic synthesis and biochemistry. For compounds with multiple potential epimeric sites, IUPAC conventions require explicit numbering of the position to avoid ambiguity, such as designating a "4-epimer" to pinpoint inversion at the fourth chiral center while maintaining the reference configuration elsewhere.^[20] This locant-based specification ensures consistency across subdisciplines, from natural product isolation to synthetic design, and is integrated into multiplicative names or fused systems where applicable.^[21]

Examples in Organic Chemistry

Epimers in Carbohydrates

In carbohydrate chemistry, epimers play a crucial role in generating structural diversity among monosaccharides, particularly within the aldohexose family. Glucose and mannose serve as classic examples of C-2 epimers, differing solely in the configuration at the C-2 chiral center. In their open-chain Fischer projections, D-glucose has the hydroxyl group at C-2 oriented to the right, while D-mannose has it to the left; this inversion leads to distinct cyclic forms in the pyranose ring, where the C-2 hydroxyl is equatorial in β-D-glucopyranose but axial in β-D-mannopyranose, influencing ring stability and interactions.^[24]/25:Biomolecules-_Carbohydrates/25.05:Cyclic_Structures_of_Monosaccharides-_Anomers) Similarly, galactose and talose exemplify epimers differing at the C-2 position, with D-talose being the C-2 epimer of D-galactose. D-Galactose, a key component of lactose (a β-1,4-linked galactose-glucose disaccharide found in milk) and blood group antigens (where it contributes to the A, B, and O antigen structures on red blood cells), features a C-4 hydroxyl configuration inverted relative to glucose. D-Talose, though rarer, shares this C-4 feature with galactose but flips the C-2 group, resulting in unique steric properties in its cyclic forms. These epimeric relationships highlight how single chiral center changes propagate through the molecule, affecting solubility and reactivity.^[25]^[26]^[27] Epimerization at C-2, as seen in glucose-mannose, significantly impacts functional properties; for instance, the equilibrium specific rotation of D-glucose is +52.7°, contrasting with +14.0° for D-mannose, reflecting their differing anomeric equilibria and hydration behaviors. This configuration also influences sweetness, with mannose exhibiting lower perceived sweetness than glucose due to variations in hydrogen bonding with taste receptors, and alters metabolic pathways, as mannose is phosphorylated to mannose-6-phosphate before isomerization to fructose-6-phosphate for entry into glycolysis, potentially diverting flux toward glycosylation rather than direct energy production.^[28]^[29] Biologically, such epimers contribute to polysaccharide diversity, enabling varied architectures in cell walls; for example, glucose forms linear cellulose in plant cell walls, while mannose and galactose incorporate into hemicelluloses and pectins for structural flexibility, and bacterial cell walls utilize epimerases to generate diverse exopolysaccharides for protection and adhesion. This epimeric variation enhances the adaptability of carbohydrate-based structures in metabolic and structural roles across organisms.^[30]

Epimers in Amino Acids

In amino acids, the D- and L-designations typically refer to enantiomers that differ in configuration at the α-carbon (C-2), representing non-superimposable mirror images rather than epimers, as epimers are diastereomers differing at only one chiral center without being overall mirror images.^[31] For standard amino acids with a single chiral center, such as alanine, the D- and L-forms are strictly enantiomers, but in cases involving additional chiral centers, true epimerism arises at non-α positions.^[32] True epimers among amino acids occur in those with β-chiral centers, such as isoleucine and threonine, where stereochemical differences at the β-carbon (C-3) produce diastereomers. Isoleucine, with the configuration (2S,3S), and its epimer alloisoleucine (2S,3R) differ solely at C-3, affecting side-chain orientation while maintaining the same α-configuration; this distinction is crucial for NMR-based identification in peptide analysis.^[33] Similarly, threonine (2S,3R) and allothreonine (2S,3S) are C-3 epimers, where the hydroxyl group on the β-carbon inverts relative to the α-amino group, influencing their incorporation into peptides and metabolic roles.^[34] In Fischer projections of these β-epimers, the α-carboxyl group is placed at the top and the α-amino on the left for L-series, with the β-carbon chain extending downward; for L-threonine, the β-hydroxyl points right, whereas in L-allothreonine, it points left, highlighting the epimeric side-chain divergence that alters steric interactions in protein environments.^[35] These configurations follow standard nomenclature for epimeric centers, denoting the differing chiral locus explicitly (e.g., threo vs. erythro series).^[36] Epimeric D-forms of amino acids are rare in eukaryotic proteins, which predominantly utilize L-isomers for standard folding and function, but they hold significance in prokaryotic structures, particularly D-alanine and D-glutamate in bacterial cell wall peptidoglycans for cross-linking and rigidity.^[31] Instances of D-allothreonine appear in bacterial metabolites and non-ribosomal peptides, such as those from Clostridium species, underscoring their role in antimicrobial natural products despite limited prevalence.^[34] Aldotetroses like erythrose and threose, which are C-3 epimers, serve as biosynthetic precursors to these amino acids through transamination pathways, linking sugar stereochemistry to amino acid diversity.^[37] The distinct configurations of threonine and allothreonine epimers can impact protein folding by altering hydrogen bonding and steric hindrance at β-positions in polypeptide chains.^[35]

Epimerization Processes

Chemical Mechanisms

Epimerization in synthetic chemistry typically involves abiotic conditions that equilibrate diastereomers differing at a single chiral center, often adjacent to a functional group like a carbonyl, through reversible deprotonation and reprotonation steps. These processes are fundamental in organic synthesis for accessing thermodynamically favored epimers without enzymatic intervention.^[38] Base-catalyzed epimerization proceeds via abstraction of a proton from the alpha-carbon adjacent to the chiral center, generating a planar enolate or enediol intermediate that allows reprotonation from either face, leading to inversion of configuration. In carbohydrates, this is exemplified by the Lobry de Bruyn–Alberda van Ekenstein transformation, where aldoses like glucose equilibrate with their C2-epimers (e.g., mannose) and ketoses (e.g., fructose) through a common 1,2-enediolate intermediate formed by deprotonation at C2 and subsequent tautomerization. The enediolate's planarity at C1–C2 enables the configurational change, with the reaction typically conducted in aqueous alkali at moderate temperatures to favor the equilibrium.^[39] The generic scheme for base-catalyzed epimerization of a 1,2-diol system adjacent to a carbonyl can be represented as:

\begin{align*} &\ce{R-CH(OH)-CH(OH)-R' ->[B^-] [R-C(OH)=C(O^-)-R'] ->[H^+] R-CH(OH)-CH(OH)-R'^*} \\ &\text{(epimerized form)} \end{align*}

^[38] Acid-catalyzed epimerization achieves similar equilibration by protonation of the carbonyl oxygen, facilitating deprotonation at the alpha-carbon to form an enol (or enol ether in some cases), which upon reprotonation can yield the epimer. This mechanism is particularly relevant for alpha-chiral carbonyl compounds, where the enol's sp² hybridization erases the stereocenter, and factors like the acidity strength and substrate electronics influence the rate. In certain systems, such as glycosides, oxocarbenium ions may form as intermediates under acidic conditions, promoting epimerization at positions alpha to the anomeric center, though this is distinct from general alpha-epimerization. Equilibrium ratios in both base- and acid-catalyzed epimerizations are governed by thermodynamic stability, with higher temperatures accelerating interconversion but potentially shifting toward less stable epimers, while pH extremes (high base or strong acid) enhance rates but may cause side reactions like degradation. Solvents like water or protic media stabilize charged intermediates, influencing selectivity; for instance, in the Lobry de Bruyn–van Ekenstein transformation, neutral to mildly basic aqueous conditions at 20–60°C yield glucose:mannose:fructose ratios of approximately 53:8:39 at equilibrium.^[38]^[39]

Enzymatic Epimerization

Enzymatic epimerization refers to the stereospecific inversion of configuration at a single chiral center catalyzed by enzymes, enabling precise control in biological systems that contrasts with the non-specific equilibrium-driven processes in chemical epimerization. These enzymes, including racemases and epimerases, facilitate the interconversion of epimers without full racemization, often through cofactor-mediated mechanisms that ensure high specificity and regulation within cellular pathways.^[40] Racemases and epimerases constitute a broad class of enzymes that catalyze the inversion of stereochemistry at chiral centers, typically in amino acids or carbohydrates, with such enzymes highly regulated, often responding to cellular demands for specific stereoisomers in protein synthesis or signaling.^[41]^[42] The general mechanism of enzymatic epimerization typically involves either the temporary opening of a cyclic structure to allow rotation and reconfiguration or cofactor-mediated hydride transfer that inverts the chiral center without complete racemization. In cofactor-dependent cases, such as those using NAD+ or pyridoxal 5'-phosphate (PLP), the enzyme binds the cofactor tightly to facilitate oxidation-reduction steps, where the substrate is oxidized to a planar intermediate (e.g., a ketone or imine), rotated, and reduced back, ensuring the reaction proceeds unidirectionally or under tight kinetic control. This specificity arises from active site geometry that positions substrates precisely, preventing off-target inversions and integrating with metabolic regulation via allosteric effectors or substrate availability.^[43]^[40] A prominent example is UDP-glucose 4-epimerase (GalE), which converts UDP-glucose to UDP-galactose by inverting the configuration at the C4 position through an NAD+-dependent hydride transfer mechanism. The enzyme first oxidizes UDP-glucose to UDP-4-ketoglucose using NAD+ as the oxidant, forming a transient NADH-bound intermediate; the planar keto group then allows rotation, followed by reduction with NADH to yield UDP-galactose, with the NAD+ regenerated in a ping-pong fashion. This process is highly specific to UDP-hexoses and regulated by substrate concentrations in nucleotide sugar pools, ensuring balanced biosynthesis.^[44]^[45] UDP-glucose 4-epimerase is essential for nucleotide sugar biosynthesis, as it interconverts UDP-glucose and UDP-galactose, precursors for glycoproteins and glycolipids; defects in this enzyme lead to epimerase deficiency galactosemia, characterized by impaired galactose metabolism and accumulation of toxic intermediates.^[46]^[47]

Biological and Practical Importance

Role in Biochemistry

Epimers play essential roles in biochemical metabolic pathways, enabling the interconversion of stereoisomers to support energy production and biosynthesis. In carbohydrate metabolism, glucose and its C2 epimer mannose are interconverted through enzymes like phosphomannose isomerase, which facilitates mannose entry into glycolysis by converting mannose-6-phosphate to fructose-6-phosphate, thereby integrating alternative sugar sources into central metabolism.^[48] Similarly, in the Leloir pathway for galactose catabolism, UDP-galactose 4-epimerase (GALE) catalyzes the reversible interconversion of UDP-galactose and UDP-glucose, ensuring galactose-derived carbons contribute to glycogen synthesis and other processes.^[46] Defects in GALE activity lead to epimerase-deficiency galactosemia, a disorder characterized by accumulation of UDP-galactose and related metabolites, resulting in symptoms such as hypotonia, liver dysfunction, and developmental delays if untreated.^[49] Epimeric variations also underpin glycoprotein diversity, influencing cell recognition and immune responses. N-acetyl-D-glucosamine (GlcNAc) and its C4 epimer N-acetyl-D-galactosamine (GalNAc) serve as key building blocks in glycan structures; for instance, in ABO blood group antigens, addition of GalNAc to the H antigen precursor by α-N-acetylgalactosaminyltransferase produces the A antigen, while GlcNAc forms part of the core type 2 chain (Gal-β1,4-GlcNAc).^[50] This epimeric distinction at the C4 position alters glycan conformation and receptor interactions, contributing to blood type specificity and transfusion compatibility. Epimerases maintain the pools of UDP-GlcNAc and UDP-GalNAc, supporting O- and N-linked glycosylation pathways essential for protein folding and cellular signaling.^[51] The stereochemical subtlety of epimers profoundly impacts enzyme-substrate interactions, often dictating specificity in binding affinity and catalytic efficiency. Such differences can modulate biological outcomes, as seen in drug design where epimer-selective inhibitors target pathogen-specific enzymes; for example, inhibitors of bacterial diaminopimelic acid epimerase disrupt peptidoglycan biosynthesis by exploiting the enzyme's preference for one epimer configuration, providing a basis for novel antibiotics against Gram-negative bacteria.^[52] This principle extends to analogs of nucleoside antibiotics like muraymycin, where epimeric modifications at key positions alter antibacterial potency and selectivity.^[53] In evolutionary terms, epimerases confer metabolic flexibility to pathogens, allowing adaptation to nutrient-limited host niches. By enabling interconversion of epimers from diverse carbon sources, these enzymes support virulence in bacteria such as Pseudomonas species, where ribulose-phosphate 3-epimerase facilitates pentose phosphate pathway flux for survival under stress.^[54] This adaptability underscores epimerases as critical for pathogenic persistence and highlights their potential as therapeutic targets.

Applications in Synthesis

In pharmaceutical synthesis, achieving epimer purity is essential for the efficacy of drugs like atorvastatin, a statin that inhibits HMG-CoA reductase to lower cholesterol levels. The active (3R,5R)-diastereomer of atorvastatin demonstrates potent inhibition of cholesterol biosynthesis, whereas its (3R,5S)-epimer at the C5 position shows significantly reduced activity, making stereoselective synthesis critical to minimize impurities and ensure therapeutic potency. Synthetic routes typically employ biocatalytic reductions or chiral auxiliary-mediated processes to favor the desired epimer with diastereomeric ratios exceeding 95:5, enabling scalable production of epimer-pure atorvastatin for clinical use.^[55] Epimerization plays a pivotal role in the total synthesis of natural product analogs, such as glycopeptide antibiotics like vancomycin, where precise control of stereochemistry at amino acid residues is required to maintain antibacterial activity. In advanced synthetic strategies, epimerization is harnessed or suppressed during macrocyclization steps to construct the rigid heptapeptide framework, avoiding the formation of diastereomeric byproducts that diminish binding to bacterial cell wall precursors. For instance, next-generation syntheses of vancomycin aglycon utilize protecting group strategies and mild base conditions to achieve >30:1 diastereoselectivity at epimerizable centers, facilitating the preparation of analogs with enhanced resistance profiles. A key technique in these applications is asymmetric synthesis employing chiral catalysts to selectively produce one epimer over its counterpart, particularly in constructing polyfunctionalized scaffolds for pharmaceuticals. Chiral transition-metal catalysts, such as rhodium-BINAP complexes, enable diastereoselective additions or hydrogenations with enantiomeric excesses often above 99%, allowing efficient access to epimer-pure intermediates in drug campaigns.^[56] This approach has been widely adopted since the 1990s for high-impact contributions in stereocontrolled synthesis. Industrially, epimer resolution through preparative chromatography, including normal-phase and reversed-phase HPLC, has become standard for purifying diastereomeric mixtures to achieve >99% purity in APIs, supporting large-scale production of stereochemically defined therapeutics.

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Mannose is far more efficiently utilized than glucose: 1.8% of transported mannose appears in N-glycans, but only 0.026% of transported glucose. At ...
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Sep 2, 2022 · Galactose epimerase (GALE) deficiency is a rare hereditary disorder of galactose metabolism with only a few cases described in the literature.
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The ABO locus has three main alleleic forms: A, B, and O. The A allele encodes a glycosyltransferase that produces the A antigen (N-acetylgalactosamine is ...
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Apr 25, 2020 · By virtue of a branched N-acylamide side chain, GalNAzMe is not interconverted by epimerization to the corresponding N-acetylglucosamine analog ...
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Apr 29, 2025 · One structure unexpectedly shows the enzyme bound to a different compound, D,L-α-methylDAP, presumably produced as a synthetic byproduct.
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Nov 3, 2018 · Nucleoside analogues have found widespread application as antiviral and antitumor agents, but not yet as antibacterials.
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Jun 11, 2024 · ... epimerase (RPE) (Figure 2). The absence of ... metabolic nodes that may underlie the high nutritional flexibility of Pseudomonas species.
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May 19, 2025 · The key chiral building block in the synthesis of atorvastatin is ethyl (R)-4-cyano-3-hydroxybutyrate, known as hydroxynitrile (HN). Annual ...
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Feb 22, 2023 · This review emphasizes the methods used for synthesizing FDA-approved chiral drugs during 2016–2020, with a special focus on asymmetric synthesis.<|separator|>