(5-Bromopyrimidin-2-yl)methanol: Handling & Use Protocol

(5-bromopyrimidin-2-yl)methanol is a brominated pyrimidine building block widely employed as a versatile synthetic intermediate in medicinal chemistry and drug discovery programs.

CAS Number

Not specified in source material — see product page for B175796

Molecular Formula

C5H5BrN2O

Molecular Weight

189.01 g/mol

Functional Groups

Primary alcohol (–CH2OH) and aryl C–Br bond on a pyrimidine ring

Key Reactivity

Undergoes cross-coupling (Suzuki, Miyaura), nucleophilic substitution, and alcohol oxidation reactions

Recommended Storage

Cool, dry place; protect from moisture and light; refer to SDS for exact conditions

Safety & Pre-Handling Considerations

(5-Bromopyrimidin-2-yl)methanol (Aladdin SKU B175796) should be handled in accordance with standard laboratory safety practices for halogenated organic compounds. Before use, consult the Safety Data Sheet (SDS) provided with the product.

Personal Protective Equipment (PPE): Wear nitrile gloves, a laboratory coat, and safety glasses at all times. If there is potential for aerosol or dust generation, use respiratory protection and work in a fume hood.

Storage: Store the reagent in a tightly sealed container in a cool, dry, well-ventilated area away from direct light and moisture. Avoid contact with strong oxidising agents and strong bases.

Waste Disposal: Dispose of all waste containing this compound according to applicable local and institutional regulations for halogenated organic waste.

Stock Solution Preparation

The primary alcohol and aryl bromide functionalities of (5-bromopyrimidin-2-yl)methanol confer moderate polarity. The following solvent guidance is based on standard solubility considerations for pyrimidine alcohols.

1. Weigh the compound: Tare a clean, dry glass vial and weigh out the required amount of B175796 on an analytical balance. Record the exact mass.
2. Select a suitable solvent: Dimethyl sulfoxide (DMSO), dimethylformamide (DMF), and methanol are generally suitable solvents for polar heterocyclic alcohols. For aqueous applications, DMSO stock solutions (e.g., 100 mM) diluted into aqueous buffer are recommended. Verify solubility empirically for your specific application.
3. Dissolve: Add solvent gradually to the weighed solid with gentle vortexing or sonication (30–60 s) until complete dissolution is observed. Avoid prolonged heating unless necessary.
4. Sterile filtration (if required): For cell-based assays, filter the stock solution through a 0.2 µm syringe filter into a sterile vessel.
5. Aliquot and store: Divide the stock solution into single-use aliquots to minimise freeze-thaw cycles. Store aliquots at –20 °C or as recommended on the product SDS. Avoid repeated freeze-thaw cycles, which may promote degradation.

Note: Specific solubility data for B175796 should be verified against the certificate of analysis (CoA) or empirically determined. Flag for review.

Synthetic Application Protocol

(5-Bromopyrimidin-2-yl)methanol is a bifunctional intermediate offering two distinct sites for chemical transformation: the aryl C–Br bond (amenable to transition-metal-catalysed cross-coupling reactions) and the primary –CH2OH group (amenable to oxidation, esterification, etherification, or conversion to the corresponding halide or leaving group).

Suzuki–Miyaura Cross-Coupling (General Guidance)

1. Combine B175796 with an arylboronic acid (1.0–1.5 equiv), a palladium catalyst (e.g., Pd(PPh3)4 or Pd(dppf)Cl2, 2–5 mol%), and a base (e.g., K2CO3 or Cs2CO3, 2–3 equiv) in a degassed solvent system (e.g., DMF/H2O or 1,4-dioxane/H2O, 4:1 v/v).
2. Heat the reaction mixture at 80–100 °C under an inert atmosphere (N2 or Ar) for 4–16 h. Monitor reaction progress by TLC or LC-MS.
3. On completion, cool to room temperature, dilute with ethyl acetate, wash with water and brine, dry over Na2SO4, filter, and concentrate under reduced pressure.
4. Purify the product by column chromatography (silica gel) or recrystallisation as appropriate.

Alcohol Functionalisation (General Guidance)

The –CH2OH group can be oxidised to the corresponding aldehyde using mild oxidants (e.g., Dess–Martin periodinane, Swern conditions, or MnO2 for benzylic-type systems) or converted to the chloride or mesylate to serve as an electrophilic coupling partner. Specific conditions should be optimised for each target molecule.

Note: All reaction conditions above are general textbook-level guidance. Specific yields, temperatures, and times for B175796 should be validated experimentally and flagged for literature citation review.

Quality Control & Analytical Verification

Before use in critical experiments, verify the identity and purity of (5-bromopyrimidin-2-yl)methanol (B175796) using the following analytical methods.

• 1H NMR: Confirm the characteristic pyrimidine ring proton signals and the –CH2OH methylene signal. The aryl C–H protons of the 5-bromopyrimidine ring appear as a singlet (two equivalent protons at positions 4 and 6). The methylene –CH2– protons appear as a singlet adjacent to the hydroxyl group. Consult the CoA for reference spectra.
• HPLC Purity: Assess purity by reversed-phase HPLC (C18 column, UV detection at 254 nm). The purity specification is stated on the product CoA; typical research-grade material is ≥95% purity.
• Mass Spectrometry: Confirm molecular weight by ESI-MS. The expected [M+H]+ or [M+Na]+ ions should be consistent with MW = 189.01 g/mol. The characteristic isotope pattern for a monobrominated compound (approximately 1:1 ratio for M and M+2 ions) should be observed.
• Melting Point: Determine and compare with the value stated on the CoA as an additional identity check.

Note: Reference spectra values should be confirmed against the Aladdin B175796 CoA. Flag for review.

Troubleshooting

The following guidance addresses common issues encountered when working with (5-bromopyrimidin-2-yl)methanol.

Problem	Possible Cause	Recommended Action
Incomplete dissolution	Insufficient solvent volume or poor solvent choice	Increase solvent volume; switch to DMSO or DMF; apply brief sonication
Low cross-coupling yield	Catalyst poisoning, insufficient degassing, or moisture	Rigorously degas solvents; use freshly prepared catalyst; ensure anhydrous conditions
Oxidation of –CH2OH during coupling	Incompatible base or oxidative conditions	Use milder base (e.g., K2CO3); reduce reaction temperature; shorten reaction time
Degradation on storage	Moisture ingress or light exposure	Store under inert gas in a desiccated, dark environment; check CoA expiry
Product purity below specification	Batch quality issue or improper handling	Contact Aladdin Scientific technical support; re-analyse by HPLC; request new CoA

Frequently asked questions

What solvents are recommended for dissolving (5-bromopyrimidin-2-yl)methanol?

DMSO, DMF, and methanol are generally suitable solvents for this polar heterocyclic alcohol. For aqueous biological assays, prepare a concentrated stock in DMSO and dilute into the aqueous medium immediately before use, keeping the final DMSO concentration below levels toxic to cells (typically ≤0.1–0.5%). Specific solubility should be confirmed empirically or from the product CoA.

Can (5-bromopyrimidin-2-yl)methanol be used directly in Suzuki–Miyaura cross-coupling reactions?

Yes. The aryl C–Br bond at the 5-position of the pyrimidine ring undergoes Suzuki–Miyaura coupling with arylboronic acids in the presence of a palladium catalyst and base. The –CH2OH group is generally compatible with standard coupling conditions, though care should be taken to avoid strongly oxidising or basic conditions that may affect the alcohol functionality.

How should (5-bromopyrimidin-2-yl)methanol be stored to ensure long-term stability?

Store B175796 in a tightly sealed container under an inert atmosphere (nitrogen or argon) in a cool, dry, dark environment. Avoid exposure to moisture, which can promote hydrolysis or degradation, and to light. Refer to the product SDS and CoA for the manufacturer's specific storage temperature recommendations and shelf life.

What is the molecular weight of (5-bromopyrimidin-2-yl)methanol and how is it used to prepare molar solutions?

The molecular weight of (5-bromopyrimidin-2-yl)methanol (C5H5BrN2O) is 189.01 g/mol. To prepare a 100 mM stock solution in 1 mL of solvent, dissolve 18.9 mg of B175796 in the chosen solvent. Scale proportionally for other concentrations or volumes. Always verify the exact weight using a calibrated analytical balance.

Is (5-bromopyrimidin-2-yl)methanol suitable as a building block in medicinal chemistry?

Yes. The compound offers two orthogonal reactive handles — the aryl bromide for cross-coupling or metal-halogen exchange, and the primary alcohol for oxidation, esterification, or conversion to a halide or leaving group — making it a versatile bifunctional building block for constructing complex pyrimidine-containing scaffolds relevant to drug discovery.

References

1. Aladdin Scientific. Product page and Certificate of Analysis for (5-Bromopyrimidin-2-yl)methanol, SKU B175796. Aladdin Scientific, Shanghai.
2. Miyaura, N.; Suzuki, A. Palladium-Catalyzed Cross-Coupling Reactions of Organoboron Compounds. Chemical Reviews 1995, 95 (7), 2457–2483. doi:10.1021/cr00039a007
3. Dess, D. B.; Martin, J. C. Readily accessible 12-I-5 oxidant for the conversion of primary and secondary alcohols to aldehydes and ketones. Journal of Organic Chemistry 1983, 48 (22), 4155–4156. doi:10.1021/jo00170a070

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