(R)-Tert-Butyl 3-Aminopyrrolidine-1-Carboxylate Hydrochloride

Dipeptidyl Peptidase-4 Inhibitor Intermediate Assembly via Pyrrolidine Urea Bond Formation

In the convergent synthesis of a DPP-4 inhibitor containing a (2R)-2-aminopyrrolidine pharmacophore, (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate hydrochloride is activated as the free amine and coupled to a triazolopiperazine urea precursor using 1,1'-carbonyldiimidazole (CDI) in tetrahydrofuran at 273 K. The target addition stoichiometry is precisely 1.00:1.00:1.15 (pyrrolidine:triazolopiperazine intermediate:CDI), with CDI charged in portions over 30 min to control gas evolution. The intermediate imidazolide is pre-formed by stirring the triazolopiperazine with CDI at 293 K for 4 h prior to slow addition of the aminopyrrolidine at ≤278 K. Agitation parameters documented for 500 L Hastelloy reactors specify an anchor impeller at 65–75 rpm to maintain suspension uniformity without inducing vortex-mediated moisture ingress. Post-coupling Boc removal proceeds via 5.5 M HCl in cyclopentyl methyl ether at 303 K, directly yielding the hydrochloride salt of the penultimate API. Specification-driven in-process controls demand determination of residual CDI activation byproducts (imidazole ≤ 0.10% w/w by GC-FID) and chiral purity of the free amine input (enantiomeric excess ≥ 99.5% by SFC, Chiralpak AD-H, CO₂:methanol 75:25, 3.0 mL/min, 220 nm). The final drug product is a phosphate monohydrate tablet at 25 mg, 50 mg, and 100 mg strengths co-formulated with metformin hydrochloride in fixed-dose combination bilayers at 50/500 mg, 50/850 mg, and 50/1000 mg label claims. Regulatory compliance encompasses ICH Q11 development guidelines with control strategy elements documented per ICH Q8(R2) design space filings, USP 〈621〉 chromatography system suitability for related substances at RRT 0.87 and 1.14, and Ph. Eur. 2.2.46 SFC methodology for enantiomeric purity.

When an (R)-3-Amino Pyrrolidine Scaffold Serves as a PARP-1/2 Inhibitor Core Fragment

The convergent assembly of a PARP inhibitor containing a 3-aminopyrrolidine-linked phthalazinone moiety exploits the chiral integrity of (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate hydrochloride during a Buchwald-Hartwig amination. A phthalazinone aryl bromide (prepared via NBS bromination in DMF at 273 K) is reacted with the Boc-protected (R)-aminopyrrolidine freebase using a Pd₂(dba)₃/Xantphos catalytic system in 1,4-dioxane at 363 K for 8 h. Catalyst loading is 0.5 mol% Pd and 1.0 mol% Xantphos relative to the aryl bromide; the base is Cs₂CO₃ at 2.0 equivalents. A production-scale observation noted that excessive palladium (above 1.0 mol%) increases debromination dimer impurity to 0.18–0.25 area%. The amine input is added at 1.30 equivalents, a deliberate excess driven by the high cost of the phthalazinone fragment. Post-reaction, a telescoped Boc cleavage using 35% aqueous HCl in 1,4-dioxane (1:3 v/v) at 318 K removes the protecting group in 1 h and simultaneously converts the product to the dihydrochloride salt, which is crystallized from ethyl acetate:ethanol (3:1). Palladium scavenging employs a trimercaptotriazine-functionalized silica cartridge (Si-TMT, 3.0 mmol/g loading) in flow-through mode at 1.5 bed volumes/min, achieving residual Pd ≤ 5 ppm per USP 〈232〉/〈233〉 by ICP-MS. The final API is a camsylate salt processed into immediate-release hard gelatin capsules at 1 mg and 5 mg strengths. Control specifications reference ICH M7(R2) limits for Pd (oral PDE 100 µg/day), and Ph. Eur. 2.4.20 for heavy metals compliance. Published data for residual bromide ion in the final isolate confirms ≤ 50 ppm by ion chromatography (IC, Metrosep A Supp 5 column, carbonate/bicarbonate eluent).

Hydrogenation of a pyridine precursor to a chiral JAK inhibitor's 3-aminopyrrolidine core is avoided in certain second-generation routes by direct incorporation of (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate hydrochloride as the pre-formed chiral synthon. The downstream process involves acylation of the pyrrolidine nitrogen after Boc removal with a pyrazolo-pyrimidine acyl chloride at 253–258 K in dichloromethane containing 3.0 equivalents of triethylamine. The acyl chloride is generated in situ from the corresponding carboxylic acid using oxalyl chloride (1.1 equivalents) with catalytic DMF (0.05 equivalents) in dichloromethane at 293 K under nitrogen. The coupling is performed in a 1000 L glass-lined reactor with retreat-curve impeller at 85 rpm; the amine hydrochloride (obtained after Boc deprotection with 4 M HCl/dioxane) is pre-dissolved in dichloromethane and added over 45 min while maintaining jacket temperature at 248 K. Published process development reports note that the free amine must be liberated in situ via triethylamine rather than pre-neutralized, as the isolated freebase undergoes intramolecular cyclization to a pyrrolidine-fused byproduct when stored for more than 2 h in solution at ambient temperature. The final active pharmaceutical ingredient is a tosylate salt processed into prolonged-release matrix tablets (5 mg and 10 mg) using a wet granulation process with hydroxypropyl methylcellulose K100M as the rate-controlling polymer. Dissolution testing per USP 〈711〉 Apparatus II (paddle, 50 rpm, pH 6.8 phosphate buffer, 900 mL, 310 K) demonstrates Q ≥ 80% at 12 h. ICH Q3D guideline requirements for elemental impurities apply, with specific controls for Pd (oral PDE 100 µg/day) and Ni (oral PDE 200 µg/day) carried forward from the acyl chloride synthesis.

An 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitor Constructed from a Chiral 3-Aminopyrrolidine Amide

Reaction of (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate hydrochloride with a pyrimidine-4-carboxylic acid derivative forms the amide core of a selective 11β-HSD1 inhibitor. The freebase, generated by partitioning between 2 M aqueous potassium carbonate and methyl tert-butyl ether, is dried azeotropically and condensed with the acid using 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC·HCl, 1.20 equivalents) and 1-hydroxybenzotriazole hydrate (HOBt·H₂O, 1.20 equivalents) in DMF at 273–278 K. The addition ratio of aminopyrrolidine freebase to acid is 1.05:1.00. Stirring proceeds for 12 h with warming to 295 K, after which the reaction mass is diluted with ethyl acetate and washed sequentially with 5% aqueous NaHCO₃ and brine. The Boc group is retained through the amide coupling and removed only after chromatography using 20% (v/v) trifluoroacetic acid in dichloromethane at 293 K for 1 h; the TFA salt is isolated by precipitation from methyl tert-butyl ether. A critical impurity identified during scale-up is the dimeric amide resulting from EDC-mediated self-condensation of the acid, which is controlled at ≤ 0.50 area% by reverse-phase HPLC (C18, acetonitrile:0.1% TFA water gradient, 1.0 mL/min, 254 nm). The final API is a hydrochloride salt of the pyrimidyl amide administered as an oral solution (2 mg/mL concentration, preserved with methylparaben 0.18% w/v and propylparaben 0.02% w/v) and as film-coated tablets at 2 mg strength. Quality attributes reference ICH Q6A decision tree #3 for particle size distribution in the micronized API (D90 ≤ 25 µm by laser diffraction, Malvern Mastersizer), and USP 〈1663〉 extractables assessment for the oral dosage form container closure system.

Incorporation of (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate hydrochloride into a CGRP receptor antagonist proceeds through a stereospecific sulfonamide coupling with a trisubstituted phenyl sulfonyl chloride in a monophasic acetonitrile-aqueous potassium phosphate buffer at pH 8.0–8.5. The freebase is generated by neutralization of the hydrochloride with 2.0 equivalents of aqueous K₃PO₄ (1.5 M) and extracted into acetonitrile. The sulfonyl chloride (prepared from the corresponding sulfonic acid using thionyl chloride with catalytic DMF at 338 K in toluene) is added at 1.02 molar equivalents to the amine at 273 K, with the pH maintained by simultaneous addition of 20% w/w aqueous K₃PO₄ via a peristaltic pump controlled by an in-line pH probe. Post-reaction, the Boc-protected sulfonamide is isolated by dilution with water and filtration, then deprotected using 4 M HCl in cyclopentyl methyl ether at 308 K to provide the amine hydrochloride. A second coupling with an indole-3-carboxylic acid fragment (HATU-mediated, 1.10 equivalents HATU, 2.5 equivalents DIPEA, DMF, 273 K) completes the bismacrocyclic framework. The final drug substance is a hemisuccinate salt formulated as a preservative-free sterile solution for subcutaneous injection in a pre-filled syringe (70 mg/mL, viscosity 8.5 cP at 298 K). Batch records from commercial finishing lines indicate that sterile filtration (0.22 µm PVDF membrane) of the bulk solution at 293 K must be completed within 4 h of reconstitution to prevent aggregation (sub-visible particles ≥ 10 µm limited to ≤ 6000 per container per USP 〈787〉). Regulatory filings reference ICH Q1A(R2) photostability data (Option 2 light source, ICH Q1B), and the bioassay specification per Ph. Eur. 2.7.1 for potency relative to the reference standard.

What Limits the Quaternary Ammonium Salt Formation in Muscarinic M3 Antagonist Quaternary Derivatives

(R)-tert-butyl 3-aminopyrrolidine-1-carboxylate hydrochloride is converted to a long-acting muscarinic antagonist bromide salt through a sequence of Boc deprotection, N-alkylation with ethyl bromide, and a final quaternization with methyl bromide. The initial deprotection uses 25% w/v hydrogen bromide in acetic acid at 293 K for 3 h, precipitating the pyrrolidine dihydrobromide salt directly. This intermediate is then selectively N-ethylated at the secondary amine using ethyl bromide (1.05 equivalents) in acetonitrile with powdered K₂CO₃ (3.0 equivalents) at 333 K in a sealed pressure vessel rated to 10 bar. The critical selectivity challenge documented at 50 kg batch size is over-alkylation to the tertiary amine quaternary salt prematurely; this is suppressed by maintaining a particle size distribution for K₂CO₃ of D50 ≤ 50 µm and monitoring conversion by ion-pair HPLC (C8 column, sodium octanesulfonate ion-pair reagent, acetonitrile:water 40:60, pH 3.0, 210 nm) to a target of ≥ 98% mono-alkylation. The final quaternization is achieved using excess methyl bromide (≤ 5.0 equivalents, condensed at 268 K) in acetone at 313 K for 48 h in a Hastelloy C-276 autoclave. Residual methyl bromide in the isolated API is controlled at ≤ 5 ppm by static headspace GC-MS (EPC Class 2 solvent limit). The final product is an inhaled micronized powder (D50 2.0–3.0 µm, delivered via a single-dose dry powder inhaler device at 15.6 µg per actuation) and a related nebulizer solution (25 µg/2.5 mL in isotonic saline). Compliance with Ph. Eur. 2.9.44 for aerodynamic particle size distribution (Next Generation Impactor at 60 L/min, fine particle fraction ≥ 35% of label claim) is mandatory. ICH Q3C(R8) residual solvent limits apply for acetone (Class 3, ≤ 5000 ppm), acetonitrile (Class 2, ≤ 410 ppm), and methyl bromide (Class 2, ≤ 5 ppm). USP 〈5.2〉 inhalation product testing and 21 CFR 211.84(c)(3) for component identity testing complete the regulatory framework.

The compound designated (R)-tert-butyl 3-aminopyrrolidine-1-carboxylate hydrochloride—systematically named (R)-3-amino-1-Boc-pyrrolidine hydrochloride—functions as a pre-activated, chirally pure secondary amine building block in medicinal chemistry and process-scale synthesis. Its molecular formula is C₉H₁₉ClN₂O₂, yielding a formula weight of 222.71 g·mol⁻¹. The material is supplied as a white to off-white crystalline powder with a melting point typically spanning 178–185 °C (decomposition) when determined by differential scanning calorimetry at a ramp rate of 10 °C·min⁻¹ under nitrogen. The specific optical rotation [α]_D²⁰ for the free base liberated from the salt is reported in the range −15° to −20° (c = 1.0, methanol), confirming the (R)-absolute configuration according to the Cahn–Ingold–Prelog convention. The hydrochloride salt form is selected over the free amine to suppress nucleophilic degradation during storage and to provide a non-hygroscopic, free-flowing solid that can be accurately dispensed under ambient humidity conditions up to 60% RH without measurable weight gain, as verified by dynamic vapor sorption analysis.

Chiral Pyrrolidine Scaffolds and the N-Boc Orthogonal Protection Strategy

The structural core consists of a five-membered pyrrolidine ring bearing a primary amine at the 3-position and a tert-butoxycarbonyl (Boc) carbamate at the 1-position. The Boc group serves as a base-stable, acid-labile protecting group that can be quantitatively cleaved with trifluoroacetic acid (TFA) in dichloromethane or with 4 M HCl in dioxane without epimerization of the stereogenic center, as monitored by chiral HPLC retention time stability. In contrast to N-benzyloxycarbonyl (Cbz) protection, which requires hydrogenolysis conditions incompatible with many late-stage functional groups, the Boc group allows orthogonal deprotection in the presence of benzyl esters, benzyl ethers, and olefinic moieties. The hydrochloride salt of the (R)-configured 3-aminopyrrolidine delivers the chiral amine directly upon neutralization with a tertiary amine base such as N,N-diisopropylethylamine (DIPEA) or triethylamine, bypassing the need for chiral resolution or asymmetric hydrogenation at the point of use. Typical commercial specifications require an enantiomeric excess (e.e.) of ≥99.0% determined by HPLC using a Chiralpak IA-3 column (4.6 × 150 mm, 3 µm) with a hexane/ethanol/diethylamine mobile phase, and a chemical purity of ≥98.0% by reverse-phase HPLC at 210 nm.

When Does the (R)-Enantiomer Offer Critical Advantage Over Racemic or (S)-Forms?

In the construction of dipeptidyl peptidase-4 (DPP-4) inhibitors and related heterocyclic pharmacophores, the (R)-3-aminopyrrolidine fragment maps directly onto the chair-like transition-state conformation that occupies the S1 and S2 pockets of the enzyme. For example, the (R)-configuration is an essential structural determinant in the potent DPP-4 inhibitor linagliptin, where the Boc-protected (R)-3-aminopyrrolidine is coupled to a xanthine core via reductive amination or nucleophilic displacement. The (S)-enantiomer, when subjected to identical coupling conditions, yields the corresponding diastereomer with a 30- to 100-fold reduction in enzyme inhibition potency, as measured by IC₅₀ shifts in fluorometric DPP-4 assays using Gly-Pro-AMC substrate. The hydrochloride salt of the (R)-enantiomer permits direct charging into reactions without the need for a separate neutralization step when the subsequent coupling employs an acid chloride or a mixed anhydride, since 1.0 equivalent of HCl is scavenged by the intrinsic basicity of the pyrrolidine nitrogen after Boc removal. This differentiates the product from the free base, which is susceptible to atmospheric CO₂ absorption and carbamate formation during extended plant-scale operations in non-inerted reactors.

From a manufacturing perspective, the (R)-enantiomer hydrochloride is produced via diastereomeric salt resolution of racemic N-Boc-3-aminopyrrolidine using (R)- or (S)-mandelic acid in isopropanol/water mixtures, a process that achieves diastereomeric excess exceeding 99% after a single recrystallization when the crystallization temperature is controlled at 0–5 °C with a cooling rate of 0.1 °C·min⁻¹. The resolved intermediate is then converted to the hydrochloride by salt exchange with a 1.0 N HCl/EtOAc solution. This resolution protocol, adapted from pilot-plant records, consistently achieves yields of 38–42% based on the racemate, limited by the solubility product of the diastereomeric salt pair. In comparison, the Cbz-protected analogue (R)-benzyl 3-aminopyrrolidine-1-carboxylate hydrochloride requires catalytic hydrogenation for N-deprotection, adding a safety barrier in facilities not rated for pressurized hydrogenation.

Solubility, Solution Stability, and Metered Addition in Continuous Flow

The hydrochloride exhibits a solubility of ≥50 mg·mL⁻¹ in water and ≥100 mg·mL⁻¹ in methanol at 20 °C, but only 2–5 mg·mL⁻¹ in tetrahydrofuran and < 1 mg·mL⁻¹ in methyl tert-butyl ether. This solubility profile dictates solvent selection for downstream amide bond formations: water-miscible polar aprotic media such as N,N-dimethylformamide (DMF) or N-methyl-2-pyrrolidone (NMP) are preferred when the reaction requires homogeneous conditions, while biphasic mixtures of dichloromethane and aqueous sodium hydroxide allow neutralization and extraction of the free base in situ. During continuous-flow amidation on a Corning Advanced-Flow reactor with a glass fluidic module of 0.5 mL internal volume, the hydrochloride is metered as a 0.5 M solution in DMF containing 1.05 equivalents of DIPEA. The preheated solution is combined with the activated carboxylic acid stream at a flow rate ratio of 1:1 and a residence time of 45 seconds at 80 °C. Under these conditions, conversion exceeds 95% with < 0.5% epimerization, as confirmed by chiral HPLC analysis of the isolated amide against an authentic racemic standard.

Solution degradation pathways are dominated by slow hydrolysis of the Boc group in acidic media and by intramolecular cyclization if the amine is liberated and left in solution without an electrophile. A stability study in 0.1 M phosphate buffer (pH 6.8) at 37 °C indicated < 2% Boc cleavage after 24 hours, as measured by LC-MS quantification of the free 3-aminopyrrolidine fragment. At pH 2.0, however, complete deprotection occurred within 4 hours. Therefore, reactions performed under aqueous acidic conditions—for instance, reductive amination with sodium cyanoborohydride at pH 4–5—require pre-neutralization of the hydrochloride with sodium acetate to prevent premature Boc loss and consequent formation of bis-alkylated pyrrolidine impurities.

Comparative Performance: Boc vs. Fmoc, Alloc, and Cbz Intermediates

A systematic evaluation of the (R)-3-aminopyrrolidine-1-carboxylate series across four N-protecting groups reveals distinct process advantages for the Boc hydrochloride in terms of crystalline handling, cost per mole, and compatibility with multi-step sequences. The table below summarizes critical parameters gathered from pilot-scale batch records and certificates of analysis.

Comparison of (R)-3-aminopyrrolidine-1-carboxylate salts and derivatives
Parameter	Boc · HCl	Cbz · HCl	Fmoc	Alloc
Physical form at 25 °C	Crystalline, free-flowing	Crystalline, moderately hygroscopic	Amorphous foam	Low-viscosity oil
Assay (HPLC area%)	≥98.0	≥97.0	≥95.0	≥93.0
Typical e.e.	≥99.5%	≥99.0%	≥99.0%	≥98.5%
Deprotection conditions	TFA/DCM or HCl/dioxane, 20 °C, 1 h	H₂, 10% Pd/C, MeOH, 3 bar, 2 h	20% piperidine/DMF, 30 min	Pd(PPh₃)₄, PhSiH₃, DCM, 15 min
Residual metal risk	Not applicable	Pd ≤ 10 ppm	Not applicable	Pd ≤ 50 ppm (requires scavenger)
Bulk pricing index (relative)	1.0	1.4	3.2	4.8

The Boc hydrochloride eliminates the need for palladium scavenging post-deprotection, which is a critical quality attribute when the final active pharmaceutical ingredient (API) is subject to ICH Q3D elemental impurity limits for palladium (oral permitted daily exposure ≤ 100 µg·day⁻¹). The Fmoc analogue, while enabling orthogonal liquid-phase peptide synthesis, introduces a dibenzofulvene by-product that must be scavenged with polymer-bound amines; additionally, the Fmoc derivative is an amorphous solid with inconsistent bulk density (0.25–0.45 g·mL⁻¹), complicating automated solid dispensing in parallel synthesis suites. The Alloc analogue requires palladium catalysis and a silane hydride source, conditions that are incompatible with substrates bearing aryl iodides or bromides due to dehalogenation side reactions.

Pyrrolidine Ring Conformation and Its Effect on Downstream Coupling Rates

The pyrrolidine ring exists in a dynamic envelope conformation where the N-Boc group imposes a bias toward the syn-orientation of the 3-amino substituent relative to the carbamate carbonyl. Variable-temperature ¹H NMR in DMSO-d₆ reveals coalescence of the diastereotopic methylene protons at the 4-position at ~340 K, corresponding to a ring-flipping barrier of approximately 48 kJ·mol⁻¹. This conformational preference places the amine in a pseudo-equatorial trajectory, enhancing its nucleophilicity in SNAr reactions with electron-deficient aromatic systems. Kinetic measurements for the displacement of a 2-chloropyrimidine substrate with the (R)-Boc-3-aminopyrrolidine (free base) in DMF at 80 °C reveal a second-order rate constant k = 1.2 × 10⁻³ M⁻¹·s⁻¹, which is approximately 2.5-fold higher than that of the corresponding piperidine derivative under identical conditions, attributed to reduced steric compression at the nitrogen lone pair.

The hydrochloride salt, when introduced directly into anhydrous DMF without pre-neutralization, exhibits a pronounced induction period in the reaction progress curve due to the slow liberation of the free base by the tertiary amine scavenger. Process analytical technology (PAT) monitoring via ReactIR 15 with a diamond ATR probe tracks the disappearance of the acid chloride C=O stretch at 1790 cm⁻¹ and the appearance of the amide C=O band at 1640 cm⁻¹. The induction period is eliminated when the hydrochloride is pre-mixed with 1.02 equivalents of DIPEA in DMF for 5 minutes prior to addition of the electrophile, a protocol adopted as standard operating procedure in kilo-lab campaigns exceeding 5 kg scale.

Storage, Handling, and Large-Scale Charge-in Safety

Long-term stability data generated under ICH Q1A guidelines (25 °C/60% RH and 40 °C/75% RH) for lots stored in double polyethylene-lined fiber drums indicate < 0.5% total impurity increase over 36 months at the long-term condition. The material is classified as non-flammable, with a dust explosion screening showing a minimum ignition energy (MIE) > 1 J and a K_St value of zero, confirming no explosion risk during pneumatic transfer or micronization. In the event of an uncontrolled exotherm during neutralization in DMF, differential scanning calorimetry on the reaction mixture identifies an exothermic onset at 210 °C with an adiabatic temperature rise (ΔT_ad) of 65 K, well within the safety margin for a vessel with 1.5× pressure relief capacity. The hydrochloride is incompatible with strong bases such as sodium hydride in aprotic solvents at temperatures above 25 °C, as deprotonation of the carbamate N–H can trigger Hoffman-type elimination to generate pyrroline by-products; if sodium hydride is required for subsequent alkylations, the Boc group should be removed first and re-installed after the basic step.

HS Code	258045
Chemical Name	(R)-Tert-Butyl 3-Aminopyrrolidine-1-Carboxylate Hydrochloride
Molecular Formula	C9H19ClN2O2
Molecular Weight	222.71
Appearance	Typically a solid (powder or crystals)
Melting Point	Specific value would require experimental determination
Solubility	Solubility characteristics depend on solvents, may be soluble in polar solvents
Purity	Can vary depending on manufacturing process, usually high purity in research - grade products
Chirality	Has (R)-configuration at the chiral center
Stability	Stable under normal storage conditions if protected from moisture and extreme temperatures
Cas Number	Specific CAS number would need to be looked up in a chemical database

Packing	100g of (R)-Tert - Butyl 3 - Aminopyrrolidine - 1 - Carboxylate Hydrochloride in sealed plastic bags.
Shipping	( R ) -Tert -Butyl 3 -Aminopyrrolidine -1 -Carboxylate Hydrochloride is shipped in well -sealed containers, following strict chemical shipping regulations. Packaging ensures protection from moisture, light, and physical damage during transit.
Storage	(R)-Tert - Butyl 3 - Aminopyrrolidine - 1 - Carboxylate Hydrochloride should be stored in a cool, dry place. Keep it away from heat sources and direct sunlight. Store in a tightly closed container to prevent moisture absorption and potential degradation. Ideal storage is in a well - ventilated area, away from incompatible substances to avoid chemical reactions.