Abstract

5-Iodowillardiine (IUPAC name: (2''S'')-2-amino-3-(5-iodo-2,4-dioxopyrimidin-1-yl)propanoic acid) is a synthetic iodinated pyrimidine derivative with molecular formula C₇H₈IN₃O₄ and molecular mass of 325.06 g·mol⁻¹. This crystalline organic compound belongs to the class of willardiine analogs characterized by a uracil ring system substituted at the 5-position with iodine and linked via a methylene bridge to an L-2-aminopropanoic acid moiety. The compound exhibits distinctive spectroscopic properties including characteristic infrared carbonyl stretching vibrations between 1650-1750 cm⁻¹ and complex NMR chemical shift patterns reflecting its heterocyclic-aromatic and amino acid components. 5-Iodowillardiine demonstrates moderate stability in aqueous solutions at neutral pH but undergoes gradual deiodination under strongly acidic or basic conditions. Its primary chemical significance derives from its role as a specialized building block in medicinal chemistry research and as a reference compound in neuropharmacological studies.

Introduction

5-Iodowillardiine represents a structurally modified amino acid derivative belonging to the willardiine class of compounds, which are characterized by a uracil moiety connected to an alanine side chain. First synthesized in the early 1990s through systematic modification of the natural product willardiine, this iodinated analog was specifically designed to enhance receptor selectivity through strategic halogen substitution. The compound is classified as an organoiodine compound and more specifically as a heterocyclic amino acid derivative. Its systematic name under IUPAC nomenclature is (2''S'')-2-amino-3-(5-iodo-2,4-dioxopyrimidin-1-yl)propanoic acid, reflecting its chiral center at the α-carbon of the amino acid portion and the substituted pyrimidine ring system. The incorporation of iodine at the 5-position of the uracil ring significantly alters the electronic properties and steric parameters compared to the parent willardiine structure, resulting in distinct chemical behavior and biological activity profiles.

Molecular Structure and Bonding

Molecular Geometry and Electronic Structure

The molecular structure of 5-iodowillardiine consists of two primary components: a 5-iodouracil moiety and an L-alanine side chain connected through a N-C bond between the uracil nitrogen at position 1 and the methylene carbon. X-ray crystallographic analysis reveals that the pyrimidine ring adopts a nearly planar configuration with bond lengths characteristic of aromatic heterocyclic systems. The carbon-iodine bond length measures approximately 2.09 Å, consistent with typical C-I single bonds in aromatic systems. The uracil ring demonstrates bond alternation with C=O bond lengths of 1.22 Å and C-N bonds of 1.38 Å, indicating significant contribution from carbonyl resonance forms.

The chiral center at the α-carbon of the alanine side chain displays (S) absolute configuration. The bond angles around this carbon atom correspond approximately to tetrahedral geometry (109.5°), with slight distortions due to intramolecular interactions. The carboxylic acid group adopts a conformation that facilitates potential hydrogen bonding with the uracil carbonyl groups. Molecular orbital calculations indicate highest occupied molecular orbitals localized primarily on the iodine atom and the uracil π-system, while the lowest unoccupied molecular orbitals are predominantly associated with the pyrimidine ring, particularly the carbonyl carbon atoms.

Chemical Bonding and Intermolecular Forces

Covalent bonding in 5-iodowillardiine follows typical patterns for aromatic heterocycles and amino acids. The carbon-iodine bond exhibits a bond dissociation energy of approximately 55 kcal·mol⁻¹, comparable to other aryl iodide systems. The uracil ring demonstrates partial double bond character between C5 and C6 (1.35 Å) and between N3 and C4 (1.35 Å), consistent with delocalized π-electron density across the heterocyclic system.

Intermolecular forces dominate the solid-state structure and solution behavior. The compound forms extensive hydrogen bonding networks through its carboxylic acid, amino, and carbonyl functional groups. The carbonyl oxygen atoms act as strong hydrogen bond acceptors, while the amino group and carboxylic acid proton serve as hydrogen bond donors. Calculated dipole moment ranges from 4.5-5.2 D, primarily oriented along the long axis of the molecule from the iodinated region toward the carboxylic acid group. Van der Waals interactions contribute significantly to crystal packing, particularly involving the iodine atom which has a van der Waals radius of 1.98 Å. The iodine substituent creates a substantial hydrophobic region that influences molecular stacking in the solid state.

Physical Properties

Phase Behavior and Thermodynamic Properties

5-Iodowillardiine typically presents as a white to off-white crystalline powder. The compound melts with decomposition at approximately 215-220 °C, though the exact melting point varies depending on heating rate and crystalline form. Differential scanning calorimetry shows an endothermic peak corresponding to the solid-phase transition followed immediately by decomposition. The heat of fusion is estimated at 28 kJ·mol⁻¹ based on calorimetric measurements.

The density of crystalline 5-iodowillardiine is 1.92 g·cm⁻³, significantly higher than non-halogenated willardiine analogs due to the presence of the heavy iodine atom. The compound is sparingly soluble in water (approximately 1.2 g·L⁻¹ at 25 °C) with solubility increasing dramatically with pH due to deprotonation of the carboxylic acid group (pKₐ = 3.8). In organic solvents, it demonstrates moderate solubility in dimethyl sulfoxide (86 g·L⁻¹) and dimethylformamide (54 g·L⁻¹), but poor solubility in hydrocarbons, ethers, and chlorinated solvents. The refractive index of crystalline material is 1.62 at 589 nm. Specific heat capacity at 25 °C is 1.2 J·g⁻¹·K⁻¹.

Spectroscopic Characteristics

Infrared spectroscopy reveals characteristic absorption bands corresponding to functional groups present. The carbonyl stretching vibrations appear as strong bands at 1695 cm⁻¹ (C2=O), 1720 cm⁻¹ (C4=O), and 1745 cm⁻¹ (COOH). N-H stretching vibrations from the amino group and uracil ring occur between 3200-3400 cm⁻¹. The C-I stretching vibration is observed as a medium-intensity band at 515 cm⁻¹.

Proton NMR spectroscopy (DMSO-d₆, 400 MHz) shows the following characteristic chemical shifts: amino acid CH-α proton at 4.25 ppm (dd, J = 7.8, 5.2 Hz), methylene protons at 3.95 ppm (dd, J = 14.2, 5.2 Hz) and 3.82 ppm (dd, J = 14.2, 7.8 Hz), uracil H-6 proton at 7.88 ppm (s), carboxylic acid proton at 12.9 ppm (br s), and amino protons at 8.35 ppm (br s). Carbon-13 NMR displays signals at 172.5 ppm (COOH), 162.3 ppm (C4=O), 151.8 ppm (C2=O), 145.6 ppm (C6), 85.3 ppm (C5), 52.8 ppm (CH-α), and 41.5 ppm (CH₂). The iodine atom causes significant downfield shifting of the C5 and C6 carbon signals compared to non-halogenated analogs.

UV-Vis spectroscopy shows absorption maxima at 288 nm (ε = 9100 M⁻¹·cm⁻¹) and 235 nm (ε = 4200 M⁻¹·cm⁻¹) in aqueous solution at pH 7.0, corresponding to π→π* transitions of the uracil chromophore. Mass spectrometric analysis exhibits a molecular ion peak at m/z 325.0 (M⁺) with characteristic fragmentation pattern including loss of iodine (m/z 198), decarboxylation (m/z 279), and cleavage of the amino acid side chain (m/z 237).

Chemical Properties and Reactivity

Reaction Mechanisms and Kinetics

5-Iodowillardiine demonstrates reactivity patterns characteristic of both iodouracil derivatives and α-amino acids. The iodine substituent activates the uracil ring toward electrophilic aromatic substitution, primarily at the C6 position, though this reactivity is somewhat attenuated by the electron-withdrawing carbonyl groups. Nucleophilic substitution reactions proceed readily at the C5 position, with iodide displacement occurring with thiols, amines, and other nucleophiles. Second-order rate constants for nucleophilic substitution with thiophenol in dimethylformamide at 25 °C is 2.3 × 10⁻³ M⁻¹·s⁻¹.

The compound undergoes photochemical deiodination upon exposure to UV light (λ < 300 nm) with quantum yield of 0.18 in aqueous solution. Thermal decomposition occurs above 200 °C via simultaneous decarboxylation and deiodination pathways. In alkaline solutions (pH > 10), hydrolysis of the uracil ring competes with deiodination, with first-order rate constants of 1.8 × 10⁻⁴ s⁻¹ and 3.2 × 10⁻⁵ s⁻¹ respectively at 25 °C. The amino acid portion demonstrates typical carboxylic acid and amine reactivity, including formation of esters, amides, and Schiff bases under appropriate conditions.

Acid-Base and Redox Properties

5-Iodowillardiine exhibits multiple acid-base equilibria corresponding to its ionizable functional groups. The carboxylic acid group has pKₐ = 3.8 ± 0.1, the amino group pKₐ = 8.2 ± 0.1, and the uracil N3-H proton pKₐ = 9.4 ± 0.2. The compound exists primarily as a zwitterion at physiological pH (7.4), with the carboxylic acid deprotonated and the amino group protonated. The isoelectric point occurs at pH 6.0.

Redox properties are dominated by the iodouracil moiety. Cyclic voltammetry in acetonitrile shows irreversible reduction waves at -1.35 V and -1.82 V vs. SCE, corresponding to sequential reduction processes. The iodine atom can be reductively removed using zinc in acetic acid or via electrochemical reduction at -0.95 V. Oxidation occurs at +1.25 V vs. SCE, primarily involving the uracil ring system. The compound demonstrates stability toward molecular oxygen in aqueous solution at neutral pH but undergoes gradual oxidation in alkaline conditions.

Synthesis and Preparation Methods

Laboratory Synthesis Routes

The most efficient laboratory synthesis of 5-iodowillardiine begins with 5-iodouracil, which is converted to the corresponding 1-(2-acetamido-2-carbethoxyethyl) derivative through N-alkylation with ethyl 2-acetamidoacrylate under basic conditions. This reaction proceeds in dimethylformamide with sodium hydride as base at 0-5 °C, achieving yields of 65-72%. Subsequent hydrolysis of both the acetamide and ester protecting groups is accomplished using 6 M hydrochloric acid at reflux temperature for 4 hours, followed by neutralization and purification by recrystallization from water-ethanol mixtures.

An alternative synthetic route involves direct electrophilic iodination of willardiine using iodine monochloride in acetic acid. This method regioselectively iodinates the 5-position of the uracil ring but requires careful control of reaction conditions to avoid over-iodination and decomposition of the amino acid moiety. Typical yields for this approach range from 45-55%. Purification is achieved through column chromatography on silica gel using chloroform-methanol-acetic acid (80:15:5) as eluent, followed by crystallization. The final product is characterized by melting point, elemental analysis, and spectroscopic methods to confirm identity and purity.

Analytical Methods and Characterization

Identification and Quantification

Analysis of 5-iodowillardiine is routinely performed by reversed-phase high-performance liquid chromatography using C18 columns with mobile phases consisting of aqueous buffers (typically 10 mM ammonium acetate, pH 4.5) and acetonitrile gradients. Detection is most commonly achieved by UV absorption at 288 nm, with a molar extinction coefficient of 9100 M⁻¹·cm⁻¹ providing quantitative determination. The limit of detection by HPLC-UV is approximately 0.1 μg·mL⁻¹, while the limit of quantification is 0.3 μg·mL⁻¹.

Capillary electrophoresis with UV detection offers an alternative separation method, particularly useful for assessing chiral purity. The compound migrates with an electrophoretic mobility of 2.8 × 10⁻⁴ cm²·V⁻¹·s⁻¹ in 25 mM phosphate buffer at pH 7.0. Mass spectrometric analysis using electrospray ionization in negative mode produces a dominant [M-H]⁻ ion at m/z 324.0, with characteristic fragment ions at m/z 198.0 (loss of HI) and m/z 152.0 (uracil carboxylate anion).

Purity Assessment and Quality Control

Common impurities in 5-iodowillardiine samples include deiodinated willardiine (typically 0.5-2.0%), starting material 5-iodouracil (0.1-0.8%), and various N-alkylated byproducts. Elemental analysis theoretical values are: C 25.87%, H 2.48%, I 39.05%, N 12.92%, O 19.68%; acceptable experimental ranges are within ±0.4% of theoretical values. Karl Fischer titration determines water content, which should not exceed 0.5% w/w in analytical samples.

Chiral purity is assessed by HPLC using chiral stationary phases or by capillary electrophoresis with chiral additives. The enantiomeric excess typically exceeds 99.5% for properly synthesized material. Residual solvent content is monitored by gas chromatography, with limits set at 500 ppm for dimethylformamide, 1000 ppm for ethanol, and 100 ppm for acetic acid. Heavy metal content, particularly other halogens, is determined by ion chromatography and should not exceed 50 ppm.

Applications and Uses

Industrial and Commercial Applications

5-Iodowillardiine serves primarily as a specialized intermediate in pharmaceutical research and development. Its commercial production remains limited to small-scale synthesis by specialty chemical suppliers, with annual global production estimated at 5-10 kg. The compound finds application as a building block for more complex molecules targeting neurological disorders, though its use in direct therapeutic applications is precluded by its chemical instability and potential toxicity.

The iodine atom provides a convenient handle for further synthetic modification, particularly through metal-catalyzed cross-coupling reactions such as Suzuki, Stille, and Sonogashira couplings. These transformations allow introduction of various aryl, alkenyl, and alkynyl substituents at the 5-position of the uracil ring, generating diverse willardiine analogs for structure-activity relationship studies. Palladium-catalyzed coupling reactions proceed with yields of 60-85% depending on the coupling partner and reaction conditions.

Research Applications and Emerging Uses

In chemical research, 5-iodowillardiine functions as a model compound for studying halogen bonding in biological systems. The iodine atom forms strong halogen bonds with oxygen and nitrogen acceptors, with bond strengths of 15-25 kJ·mol⁻¹, making it valuable for investigating these interactions in molecular recognition processes. Crystallographic studies of 5-iodowillardiine complexes with various receptors have provided fundamental insights into halogen bonding geometry and energetics.

Emerging applications include use as a template for designing metal-organic frameworks and as a ligand for transition metal complexes. The multiple coordination sites (carbonyl oxygen atoms, amino group, carboxylic acid, and iodine) allow diverse binding modes with metal ions. Copper(II) complexes of 5-iodowillardiine have been characterized and exhibit interesting magnetic properties due to exchange interactions between metal centers mediated by the organic ligand.

Historical Development and Discovery

5-Iodowillardiine was first synthesized in 1992 as part of systematic structure-activity relationship studies on excitatory amino acid receptors. Researchers sought to modify the natural product willardiine, isolated from Acacia willardiana, to enhance receptor subtype selectivity. The introduction of halogen substituents, particularly at the 5-position of the uracil ring, was hypothesized to influence binding affinity through electronic and steric effects.

Initial synthetic approaches adapted methods developed for 5-halouracil nucleosides, with key innovations in protecting group strategy and reaction conditions to preserve the chiral integrity of the amino acid portion. The first reported synthesis employed direct iodination of protected willardiine derivatives using N-iodosuccinimide, though later methods proved more efficient and scalable. Characterization of the compound in the early 1990s established its basic physicochemical properties and provided the foundation for subsequent chemical studies.

Conclusion

5-Iodowillardiine represents a chemically interesting modified amino acid that combines features of heterocyclic chemistry, halogen chemistry, and amino acid biochemistry. Its molecular structure exhibits complex electronic properties due to the interplay between the electron-withdrawing iodine substituent and the conjugated uracil system. The compound serves as a valuable synthetic intermediate and research tool, particularly for investigating halogen bonding interactions and designing receptor-selective analogs. Future research directions likely include development of improved synthetic methodologies, exploration of coordination chemistry with various metal ions, and application as a building block for more complex molecular architectures. The fundamental chemical properties of 5-iodowillardiine continue to provide insights into structure-property relationships in halogenated heterocyclic compounds.