Fmoc-D-2-Thienylalanine: Properties, Uses & FAQs

Fmoc-D-2-thienylalanine is a non-natural, Fmoc-protected D-amino acid bearing a 2-thienylmethyl side chain, widely used as a building block in solid-phase peptide synthesis to introduce conformational constraint and metabolic stability into peptidomimetic sequences.

Chemical Name

Fmoc-D-2-thienylalanine (Nα-Fmoc-D-3-(2-thienyl)alanine)

SKU

F182573

Protecting Group

9-Fluorenylmethoxycarbonyl (Fmoc) on the α-amine

Stereochemistry

D-configuration at the α-carbon

Side Chain

2-Thienylmethyl (heterocyclic thiophene ring at position 2)

Primary Application

Solid-phase peptide synthesis (SPPS) building block for peptidomimetics

Recommended Storage

Store at 2–8 °C under dry, inert conditions; protect from moisture and light

What Is Fmoc-D-2-Thienylalanine?

Fmoc-D-2-thienylalanine is a non-proteinogenic, Fmoc-protected amino acid in which the side chain of alanine is replaced by a 2-thienylmethyl group—a five-membered aromatic heterocycle containing a sulfur atom at position 1 and a methylene linkage at position 2. The α-amine is protected by the base-labile 9-fluorenylmethoxycarbonyl (Fmoc) group, making it directly compatible with standard Fmoc solid-phase peptide synthesis (SPPS) workflows.

The D-configuration at the α-carbon distinguishes this compound from its L-enantiomer. D-amino acids are resistant to most mammalian proteases, so their incorporation confers enhanced metabolic stability and can enforce specific backbone conformations in the resulting peptide. The thiophene ring is bioisosteric with a phenyl ring and offers favorable π-stacking and hydrophobic interactions, making Fmoc-D-2-thienylalanine valuable in medicinal-chemistry-oriented peptide libraries.

Chemical Properties and Specifications

Fmoc-D-2-thienylalanine (SKU F182573) is supplied by Aladdin Scientific for research use. Key physicochemical characteristics are summarized below:

• Molecular formula: C₂₂H₁₉NO₄S
• Molecular weight: approximately 409.46 g/mol
• Appearance: white to off-white crystalline powder
• Solubility: soluble in DMF, DMSO, and dichloromethane; sparingly soluble in water
• Fmoc group removal: achieved with 20% piperidine in DMF (standard Fmoc deprotection)
• Optical activity: D-configuration; specific rotation will be negative relative to the L-enantiomer

Purity specifications and exact lot-specific data (including HPLC purity, specific rotation, and water content) are provided on the Certificate of Analysis (CoA) accompanying each shipment. Researchers should consult the CoA before use.

Applications in Solid-Phase Peptide Synthesis

Fmoc-D-2-thienylalanine is primarily used as a building block in Fmoc-based SPPS on resins such as Wang, Rink Amide, or 2-chlorotrityl chloride resin. Its incorporation follows the same coupling chemistry as standard Fmoc amino acids:

1. Activation: Couple using standard reagents such as HATU/DIPEA, HBTU/HOBt/DIPEA, or DIC/Oxyma in DMF or NMP.
2. Deprotection: Remove the Fmoc group with 20% piperidine in DMF (2 × 5–10 min).
3. Cleavage and global deprotection: Standard TFA-based cocktails are compatible.

Typical applications include:

• Synthesis of protease-stable peptidomimetics for drug-discovery programs
• Construction of peptide libraries to explore structure–activity relationships (SAR) involving D-amino acid substitution
• Preparation of fluorescent or heterocyclic-containing peptide probes
• Introduction of a thiophene pharmacophore as a phenyl bioisostere in lead optimization

Because D-amino acids can disrupt β-sheet aggregation, incorporation of Fmoc-D-2-thienylalanine can also improve the overall solubility and handleability of otherwise aggregation-prone sequences.

Storage, Handling, and Safety

Storage: Store Fmoc-D-2-thienylalanine at 2–8 °C in a tightly sealed container under dry, inert atmosphere (e.g., argon or nitrogen). Protect from moisture, heat, and prolonged light exposure. Proper storage preserves the integrity of both the Fmoc protecting group and the thienyl side chain.

Handling: Use standard laboratory precautions: gloves, lab coat, and safety glasses. Weigh the compound in a chemical fume hood to avoid inhalation of fine powder. If contact with skin or eyes occurs, rinse thoroughly with water and seek medical advice if irritation persists.

Stability: When stored correctly, the compound is stable for the shelf life indicated on the product label. Avoid repeated freeze–thaw cycles for dissolved stock solutions. Prepare fresh SPPS coupling solutions on the day of use to minimize racemization and reagent degradation.

Disposal: Dispose of waste in accordance with local institutional and governmental regulations for organic chemical waste.

Refer to the product Safety Data Sheet (SDS) available from Aladdin Scientific for complete hazard classification and regulatory information.

Frequently asked questions

What is the difference between Fmoc-D-2-thienylalanine and Fmoc-L-2-thienylalanine?

The two compounds are enantiomers that differ in the stereochemical configuration at the α-carbon: the D-form has the R-configuration (by CIP rules for this residue) while the L-form has the S-configuration. In peptide synthesis, D-amino acids introduce resistance to proteolytic degradation and can impose distinct backbone conformations compared to L-amino acids. For most biological assays, the two enantiomers will exhibit different pharmacological and biological profiles.

Which coupling reagents and conditions are recommended for incorporating Fmoc-D-2-thienylalanine in SPPS?

Standard Fmoc-SPPS coupling reagents such as HATU, HBTU, or DIC/Oxyma in DMF or NMP are suitable, typically using 3–5 equivalents of the amino acid relative to resin loading with DIPEA as base. Because D-amino acids can be more prone to racemization under forcing conditions, milder reagents and shorter coupling times are preferable; DIC/Oxyma is frequently recommended for sterically hindered or epimerization-sensitive residues. Always monitor coupling efficiency by colorimetric tests (e.g., Kaiser test) or HPLC analysis of cleaved peptides.

How should I store Fmoc-D-2-thienylalanine to maintain its quality over time?

Store the compound at 2–8 °C in a tightly closed container under an inert atmosphere, protected from moisture and light. Moisture can cause degradation of the Fmoc carbamate linkage, while light exposure may affect the compound over extended periods. For stock solutions dissolved in DMF or DMSO, prepare small aliquots to avoid repeated freeze–thaw cycles and use within a reasonable timeframe. Always consult the CoA for the specific lot's recommended shelf life.

Is Fmoc-D-2-thienylalanine suitable for use as a phenylalanine bioisostere in peptide drug discovery?

Yes. The 2-thienyl ring is a well-established bioisostere for the phenyl group, sharing a similar size, planarity, and aromatic character while offering a different hydrogen-bond-acceptor profile due to the ring sulfur atom. Replacing L- or D-phenylalanine with D-2-thienylalanine can modulate receptor binding, improve selectivity, or alter metabolic properties. This strategy is commonly employed in medicinal chemistry programs targeting GPCRs, proteases, and other peptide-binding proteins.

What solvents are compatible with Fmoc-D-2-thienylalanine for preparing coupling solutions?

Fmoc-D-2-thienylalanine is soluble in polar aprotic solvents commonly used in SPPS, including DMF (N,N-dimethylformamide), NMP (N-methylpyrrolidone), and DMSO. Dichloromethane (DCM) can also be used as a co-solvent. Aqueous systems are generally avoided for coupling steps due to poor solubility in water and potential Fmoc hydrolysis. Always prepare coupling solutions fresh on the day of use.

References

1. Carpino, L.A. & Han, G.Y. (1972). The 9-fluorenylmethoxycarbonyl amino-protecting group. Journal of Organic Chemistry, 37(22), 3404–3409. doi:10.1021/jo00795a005
2. Fields, G.B. & Noble, R.L. (1990). Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids. International Journal of Peptide and Protein Research, 35(3), 161–214. PMID:2191922
3. Aurelio, L., Brownlee, R.T.C., & Hughes, A.B. (2004). Synthetic preparation of N-methyl-amino acids. Chemical Reviews, 104(12), 5823–5846.
4. Aladdin Scientific Product Page: Fmoc-D-2-thienylalanine, SKU F182573. Aladdin Scientific.

Products are supplied for research and development use only. Not for use in humans, animals, diagnosis, or therapy.