cis-3,5-Dimethylmorpholine HCl: Properties & Lab FAQs

cis-3,5-dimethylmorpholine hydrochloride is a stereodefined, salt-stabilized heterocyclic amine building block widely used in medicinal chemistry and synthetic research as a chiral morpholine fragment.

Chemical Name

cis-3,5-dimethylmorpholine hydrochloride

Aladdin SKU

C174523

Core Scaffold

Six-membered morpholine ring (oxygen and nitrogen heteroatoms) with cis methyl substituents at the 3- and 5-positions

Physical Form

Typically a white to off-white crystalline solid (hydrochloride salt)

Stereochemistry

cis relative configuration; both methyl groups on the same face of the morpholine ring

Typical Application

Medicinal chemistry building block, fragment-based drug discovery, N-alkylation and acylation reactions

What Is cis-3,5-Dimethylmorpholine Hydrochloride?

cis-3,5-Dimethylmorpholine hydrochloride (Aladdin SKU: C174523) is the hydrochloride salt of cis-3,5-dimethylmorpholine, a six-membered saturated heterocycle containing one oxygen and one nitrogen atom in the ring. The cis designation indicates that both methyl substituents at the 3- and 5-positions occupy the same face of the ring, conferring a defined relative stereochemistry that distinguishes it from the trans isomer.

Converting the free base to its hydrochloride salt improves crystallinity, bench stability, and ease of weighing, which are all practical advantages for research use. In solution, the salt readily dissociates to release the free amine upon adjustment to basic pH, making it straightforward to use in downstream synthetic steps.

Solubility, Storage, and Handling

Solubility: As a hydrochloride salt, cis-3,5-dimethylmorpholine hydrochloride is expected to show good solubility in water and polar protic solvents such as methanol and ethanol. Solubility in non-polar organic solvents is typically low. For anhydrous reaction conditions, dissolving in dimethylformamide (DMF) or dimethyl sulfoxide (DMSO) with warming may be appropriate, though users should verify compatibility with their specific protocol.

Storage: Store the compound in a tightly sealed container under cool, dry conditions, away from moisture and incompatible materials such as strong oxidizers and strong acids. Refrigerated storage (2–8 °C) is commonly recommended for amine salts to maximize long-term stability, but always consult the product-specific Certificate of Analysis (CoA) or Safety Data Sheet (SDS) supplied by Aladdin Scientific for authoritative guidance.

Handling: Use standard laboratory precautions: work in a well-ventilated area or fume hood, wear appropriate personal protective equipment (gloves, eye protection, lab coat), and avoid inhalation of dust. Consult the SDS before first use.

Applications in Synthesis and Medicinal Chemistry

The morpholine ring is a privileged scaffold in drug discovery due to its favorable physicochemical properties, including moderate lipophilicity, hydrogen-bond acceptor capacity, and metabolic stability relative to acyclic amines. The introduction of cis-3,5-dimethyl substitution adds steric and conformational control, which can modulate binding affinity, selectivity, and metabolic profile of target compounds.

cis-3,5-Dimethylmorpholine hydrochloride serves as a building block for:

• N-Acylation reactions — coupling with carboxylic acids or acid chlorides to form morpholine amides.
• N-Alkylation reactions — reductive amination or alkylation to append the morpholine fragment to carbon frameworks.
• Fragment-based drug discovery — the constrained ring conformation provides a defined three-dimensional shape for structure–activity relationship (SAR) exploration.
• Asymmetric synthesis auxiliaries — chiral morpholine derivatives can serve as templates or resolving agents.

Researchers should free the base from the hydrochloride salt (e.g., with aqueous base extraction or use of a solid-phase carbonate scavenger) when reactions require the neutral amine form.

Purity, Specification, and Quality Assurance

Aladdin Scientific provides cis-3,5-dimethylmorpholine hydrochloride (C174523) as a research-grade reagent. Each lot is accompanied by a Certificate of Analysis (CoA) detailing identity confirmation, purity assessment method, and lot-specific results. Researchers requiring higher purity grades or custom specifications are encouraged to contact Aladdin's technical support team.

Key quality parameters typically reported for this class of compounds include:

• Purity by HPLC or titration
• Identity by NMR or mass spectrometry
• Appearance (color and physical form)
• Water content (Karl Fischer, where applicable)

Always download the current CoA for your specific lot number from the product page or by contacting customer service, as specifications may vary between lots.

Ordering and Customer Support

cis-3,5-Dimethylmorpholine hydrochloride is available from Aladdin Scientific under SKU C174523. To place an order:

1. Search for C174523 or the full product name on the Aladdin Scientific website.
2. Select the desired quantity and packaging format.
3. Add to cart and proceed through the standard checkout. Purchase orders are accepted for institutional customers.

For technical questions about the compound's suitability for your application, purity requirements, bulk pricing, or custom synthesis inquiries, contact Aladdin's technical support or sales team via the website contact form or customer service email. Returns and refunds are handled according to Aladdin's standard return policy — please review the relevant policy page or contact customer service for details specific to chemical reagents.

Frequently asked questions

What is the difference between cis- and trans-3,5-dimethylmorpholine?

In cis-3,5-dimethylmorpholine, both methyl groups at the 3- and 5-positions are on the same face of the morpholine ring, while in the trans isomer they are on opposite faces. This stereochemical difference affects the ring conformation, dipole moment, and three-dimensional shape, which in turn can significantly influence binding interactions in biological targets and physicochemical properties such as lipophilicity.

How do I convert cis-3,5-dimethylmorpholine hydrochloride to the free base for use in reactions?

The free base can be liberated by treating an aqueous solution of the hydrochloride salt with an aqueous base (e.g., sodium hydroxide or potassium carbonate solution) and extracting the free amine into a suitable organic solvent such as ethyl acetate or dichloromethane. Alternatively, when working in DMF or DMSO-based reaction mixtures, adding a non-nucleophilic base (e.g., triethylamine or Hünig's base, DIPEA) in slight excess directly to the reaction is a common in-situ approach to neutralize the HCl and generate the reactive free amine.

What are the recommended storage conditions for C174523?

As a general guideline for hydrochloride salts of secondary amines, store C174523 in a tightly sealed container in a cool, dry location away from moisture, light, and incompatible substances. Refrigerated storage at 2–8 °C is commonly used for such reagents to maximize shelf life. Always refer to the current Safety Data Sheet (SDS) and Certificate of Analysis (CoA) available from Aladdin Scientific for the authoritative, lot-specific storage recommendation.

Is cis-3,5-dimethylmorpholine hydrochloride suitable for GMP or clinical use?

C174523 is supplied as a research-grade reagent and is intended for laboratory research use only. It is not manufactured under GMP conditions and is not suitable for direct use in clinical, diagnostic, or therapeutic applications. Researchers requiring GMP-grade material should contact Aladdin Scientific's sales team to discuss availability, custom synthesis options, or referral to appropriate GMP suppliers.

Can I request a Certificate of Analysis or Safety Data Sheet for C174523?

Yes. Certificates of Analysis (CoA) and Safety Data Sheets (SDS) for C174523 are available through the Aladdin Scientific website product page. You can download documents directly by entering your lot number, or contact customer service if the document for your specific lot is not yet posted online. Reviewing the SDS before handling any chemical is strongly recommended.

References

1. Aladdin Scientific product page for cis-3,5-dimethylmorpholine hydrochloride, SKU C174523.
2. Vitaku, E.; Smith, D. T.; Njardarson, J. T. Analysis of the structural diversity, substitution patterns, and frequency of nitrogen heterocycles among U.S. FDA approved pharmaceuticals. J. Med. Chem. 2014, 57, 10257–10274. doi:10.1021/jm501100b
3. Carey, F. A.; Sundberg, R. J. Advanced Organic Chemistry, Part A: Structure and Mechanisms, 5th ed.; Springer: New York, 2007.

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