GRADE & PURITYReagent Grade?General reagent-grade purity suitable for most laboratory work. Use as a dependable default when no specific higher grade is required.
This compound belongs to the class of organic compounds known as alkyl aryl ethers. These are organic compounds containing the alkyl aryl ether functional group with the generic formula R-O-R' , where R is an alkyl group and R' is an aryl group.
External Descriptors
Not available
1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.
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Recensioni
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Application Protocols
Not applicable. No tested biological assay protocols (e.g., WB, IHC, IF, FC) are provided for this small-molecule reagent. Typical “protocols” relate to synthetic procedures; see the Reaction Conditions tab for representative literature-style guidance.
Biological Roles
General context (informational; not product-specific; no clinical claims)
The pyrimidine ring is a fundamental heteroaromatic motif present in nucleic acid bases (cytosine, uracil, thymine), numerous cofactors, and bioactive small molecules. Substitution at C2 modulates basicity, hydrogen-bonding patterns, and electronics that govern recognition in protein “hinge” or nucleic-acid binding sites.
A 2-methoxy substituent reduces acidity at adjacent carbons and alters dipole and hydrogen-bond acceptor strength relative to hydroxy or amino substituents. This can influence permeability, solubility, and metabolic stability of analogs built from this scaffold.
In biochemical probe development, 2-alkoxy pyrimidines often serve as masked electrophiles/handles: the 2-OR can be exchanged for amines or thiols to generate libraries of 2-substituted pyrimidines for SAR exploration.
Practical implication for researchers
Use 2-methoxypyrimidine as a platform to access 2-amino, 2-thio, and 2-alkyl derivatives for studying heteroaromatic recognition in enzymes, kinases, or nucleic-acid interacting proteins in vitro.
Note: This product is for research use only (Product Data) and is not intended for human or animal therapeutic or diagnostic use.
Buffer Applications
This compound is a neutral/weakly basic heteroaromatic building block and is not used as a buffering agent.
Not typically applicable: It lacks a conjugate acid/base pair with an aqueous pKa in the physiological buffering window suitable for high-capacity buffers.
Guidance: For aqueous biochemical work, prepare solutions in appropriate buffers (e.g., phosphate, HEPES) and dissolve this compound first in a miscible co-solvent (MeCN, DMSO) if needed before dilution.
Green Alternatives
While 2-methoxypyrimidine itself is the target reagent, greener choices can be made around its use and synthesis.
Greener solvent choices (for SNAr and metalation)
Prefer MeCN, 2-MeTHF, or CPME over DMF/DMSO/NMP when feasible to reduce EHS burdens and simplify workup.
For high-temperature SNAr, propylene carbonate can be an effective polar aprotic alternative with low volatility.
Avoid halogenated activation where possible
Using 2-OMe as a leaving group (SNAr or Ni-catalyzed C–O activation) can circumvent halogenated electrophiles (e.g., 2-chloro/2-fluoro pyrimidines), reducing halide waste.
Energy and waste minimization
Employ microwave-assisted SNAr to shorten reaction times and cut energy input.
DMF/DMSO: high rate/solubility; difficult removal; higher EHS concerns.
MeCN/2-MeTHF/CPME: lower toxicity, easier removal; may need higher temperature or longer time.
Halogenated reagents (2-Cl/2-F pyrimidines): very reactive but generate halide waste.
2-OMe precursor: halogen-free handle; may require catalysts or stronger bases.
Implement solvent swaps and intensified heating (microwave/flow) to maintain productivity while improving process mass intensity.
Pharmaceutical Uses
Research-use note: For research use only (Product Data). No medical or clinical claims are made.
Role in pharma R&D/manufacturing (informational)
Intermediate: 2-Methoxypyrimidine serves as a halogen-free electrophile surrogate at C2 to generate 2-substituted pyrimidines (amines, thioethers), common motifs in kinase inhibitors, antivirals, and CNS candidates.
Fragment/scaffold: The pyrimidine core is a privileged scaffold for hinge-binding motifs in kinases; the 2-OMe variant can be elaborated late-stage.
Impurity/analytical reference: May be used as a process impurity marker or reference standard in routes that employ alkoxy-protected pyrimidines.
Formulation/excipient status
Not an excipient; no pharmacopeial monograph known for this specific derivative (literature context). Any use in GMP settings requires appropriate qualification and specifications.
For regulated applications, establish specifications (assay, residuals, metals) and analytical methods per ICH Q6/Q3 guidance.
Physical Properties
Item-specific specs
Appearance: Not specified for this item; refer to CoA/Spec Sheet.
Exact BP/MP/density/RI/UV cutoff/assay: Not specified for this item; refer to CoA/Spec Sheet.
Literature/general properties for the pyrimidine/alkoxy-diazine class (non-spec for this item)
Phase: low-molecular-weight heteroaromatic; many 2-alkoxypyrimidines are low-melting solids or mobile liquids at ambient conditions.
Polarity: moderately polar (one ether O and two ring nitrogens); good H-bond acceptor; no H-bond donors.
Basicity: weakly basic heteroaromatic; conjugate-acid pKaH of the pyrimidine core typically ~1–2 (literature, unsubstituted pyrimidine), with electron-donating substituents slightly increasing basicity.
Solubility behavior: miscible or highly soluble in common polar organics (EtOAc, MeCN, THF, alcohols, DCM) and variably soluble in nonpolar hydrocarbons; limited solubility in water expected for many alkoxy-diazines.
Volatility: expected moderate volatility relative to higher MW heteroaromatics; handle in a fume hood.
Spectroscopy: UV absorption typical of diazines (π→π* around 230–280 nm; literature, scaffold-dependent). 1H/13C NMR show downfield ring CH at C4/C5/C6 and a singlet for O–CH3.
Note: For project-critical numerical specifications (bp, mp, density, water/peroxide/metal limits), consult the item’s CoA/Spec Sheet.
Quality and Grades
Item-specific quality
Grade: Reagent Grade (Product Data). This denotes suitability for general laboratory synthesis and analysis. It is not necessarily optimized for trace analysis, chromatography baselines, or biocompatibility without further purification.
Assay, residual solvents, water, metals, UV cutoff: Not specified for this item; refer to CoA/Spec Sheet.
Practical implications
Reagent Grade typically supports routine synthetic transformations (e.g., substitutions, metalations) and method development.
For sensitive catalysis (e.g., ppm-level Pd/Ni), photoredox, or structure–activity studies where trace impurities may matter, consider verifying by GC/LC, drying or distilling if applicable, or contacting us for higher-spec material.
If low UV background is critical (analytical HPLC/UV), evaluate a test blank; Reagent Grade is not inherently “HPLC grade.”
Stabilizers and additives
Any stabilizers or inhibitors: Not specified for this item; refer to CoA/Spec Sheet.
Documentation
Each lot ships with/has available a Certificate of Analysis. For project-critical attributes (assay, residuals, water, elemental impurities), use the lot-specific CoA/Spec Sheet.
Reaction and Applications
2-Methoxypyrimidine is a versatile diazine building block. The electron-poor ring (N1,N3) activates ipso positions, while the 2-methoxy can be leveraged as a leaving group or a directing handle.
Nucleophilic aromatic substitution (SNAr)
The C2 position between two ring nitrogens is highly activated. Under sufficiently basic and/or high-temperature conditions, 2-OMe can be displaced by N-, O-, or S-nucleophiles to access 2-substituted pyrimidines (e.g., amination, thiolation, alkoxylation). Amination often benefits from strong bases (alkoxides, alkali carbonates, DBU) and polar aprotic solvents.
C–O bond activation chemistry
Nickel catalysts (e.g., Ni(0)/NHC or phosphine ligands) can enable cross-couplings from aryl/heteroaryl methyl ethers via C–O activation. This provides a halogen-free entry to C–C or C–N bond formation at C2, complementing more common 2-chloro/2-fluoro pyrimidines.
Directed metalation and electrophilic trapping
The diazine ring is amenable to regioselective deprotonation (often at C5) with LDA/s-BuLi in ethereal solvents at low temperature. Subsequent quench with electrophiles (carbonyls, halogens, CO2) elaborates the scaffold.
Cross-coupling after activation
When 2-OMe is retained, halogenation at C4/C5/C6 (literature methods) enables Suzuki–Miyaura, Buchwald–Hartwig, or Negishi couplings orthogonal to the 2-position.
Applications
Synthesis of nucleobase analogs, kinase hinge-binding fragments, and heteroaromatic libraries; a convenient precursor to 2-aminopyrimidines and 2-thiopyrimidines via SNAr.
Notes: Selectivity depends on base, solvent, and temperature. Perform microscale screens to balance rate vs. competing ring addition/elimination.
Reaction Conditions
General literature-style guidance for transformations of 2-alkoxypyrimidines (informational; adjust per project and verify experimentally):
Base: K2CO3/Cs2CO3 (2–3 equiv) or DBU (1–2 equiv).
Temperature/time: 80–140 °C, 2–24 h (oil bath or sealed tube/microwave).
Notes: stronger nucleophiles (amines, thiolates) react faster; methoxide departure may require elevated T. Monitor by LC–MS.
Thiolation at C2
Nucleophile: NaS–R (generated in situ from RSH + NaH/K2CO3).
Solvent: DMF/DMSO or MeCN; 60–120 °C.
Caution: avoid air to limit disulfide formation.
Ni-catalyzed C–O activation (C–N/C–C coupling)
Catalyst: Ni(cod)2 (2–10 mol%) with NHC or bulky phosphine ligand; base: KOt-Bu/NaOt-Bu or Zn/Mg reagents (for Kumada/Negishi).
Solvent: dioxane, toluene, anisole, 2-MeTHF; 80–140 °C.
Notes: exclude air/moisture; oxidative addition into Ar–OMe is ligand-dependent.
Directed lithiation (C5 functionalization)
Base: LDA or s-BuLi (1.1–1.5 equiv) in THF/2-MeTHF at −78 to −20 °C.
Electrophiles: CO2, DMF, I2/Br2, RCHO.
Quench: careful, low-temperature aqueous NH4Cl.
These conditions are representative literature practices and are not item-specific specifications.
Safety and Handling
Item-specific hazard listing
GHS Classification, pictograms, signal word, H-statements: Not specified for this item; refer to SDS.
General safety guidance for heteroaromatic ethers (informational; defer to SDS)
Likely hazards: flammable liquid/vapor and irritant are common for small heteroaromatics; avoid ignition sources; ensure ventilation.
PPE: lab coat, safety glasses or splash goggles, nitrile gloves; use in a certified fume hood.
Handling: minimize inhalation and skin contact. Transfer under local exhaust; use grounded/antistatic techniques if flammable. Prevent contact with strong oxidizers and strong acids/bases that may induce decomposition or substitution.
First aid (overview):
Inhalation: move to fresh air; seek medical attention if symptoms persist.
Skin/eye: rinse with water for at least 15 minutes; remove contaminated clothing; obtain medical advice if irritation continues.
Ingestion: rinse mouth; do not induce vomiting; seek medical attention.
Spill response: eliminate ignition sources; absorb with inert material (vermiculite, sand); collect in labeled waste; ventilate area.
Storage: keep tightly closed at room temperature per Product Data; segregate from strong oxidizers; store in a cool, dry, well-ventilated place.
Always consult the product-specific SDS for authoritative hazard classification and response measures.
Solvent Selection
This product is a heteroaromatic building block rather than a solvent. Solvent choice is therefore about dissolving it efficiently and enabling its reactions.
Polarity and miscibility (general guidance)
Likely high solubility in polar organics: acetonitrile, DMF/DMAc, DMSO, THF, dioxane, EtOAc, MeOH/EtOH; moderate in DCM/CHCl3; limited in alkanes.
For nucleophilic substitutions on the pyrimidine ring, polar aprotic solvents (DMF, DMSO, NMP, MeCN) typically accelerate SNAr and C–O activation chemistry.
Practical selection by transformation type (informational)
SNAr with amines/thiols: DMSO, DMF, NMP, or MeCN; add base (e.g., K2CO3, Cs2CO3, DBU) and heat as needed.
Directed metalation at C5: ethereal solvents (THF, 2-MeTHF) at −78 to 0 °C with LDA/s-BuLi, then quench with electrophiles.
Cross-coupling via C–O activation (Ni-catalyzed): CPME, 2-MeTHF, dioxane, toluene, or anisole under elevated T may be suitable; coordinate with ligand/base system.
Comparison notes
DMF/DMSO maximize rate/solubility but pose EHS burdens and challenging workups; MeCN and 2-MeTHF often provide greener, lower-boiling alternatives with good performance.
For solubility numbers or partition data, consult the lot CoA or perform a small-scale solubility screen.
Storage and Reconstitution
Item-specific storage (from Product Data)
Storage conditions: Room temperature. Keep container tightly closed in a dry, well-ventilated place.
Shipped in: Not specified for this item; refer to CoA/Spec Sheet.
Practical handling
Protect from moisture and strong oxidizers. Use clean, dry tools/syringes for aliquots to avoid adventitious water or base/acid contamination that could promote substitution or degradation.
If solidifying/crystallizing upon cold storage, gently warm to ambient and swirl to homogenize before sampling.
Solution preparation
Reconstitution: Not applicable; supplied neat. To prepare stock solutions, dissolve in a compatible organic solvent (e.g., MeCN, DMSO, THF, DCM, alcohols) at desired concentration. Filter through PTFE (0.2 µm) if particulate is observed.
Stability of solutions: For highest integrity, prepare fresh. If storage of solutions is required, keep in amber vials under inert gas at 2–8 °C and test for stability prior to use.
Always consult the SDS and lot-specific CoA/Spec Sheet for definitive storage and stability guidance.
Structure and Identity
Professional summary for a heteroaromatic building block used in synthesis.
Item-specific (from Product Data)
Product name: 2-Methoxypyrimidine (SKU: M479782)
CAS: 931-63-5
Grade/Purity: Reagent Grade
Storage conditions: Room temperature
SMILES: Not specified for this item; refer to CoA/Spec Sheet.
InChIKey: Not specified for this item; refer to CoA/Spec Sheet.
Literature/computed identifiers and description (non-spec for this item)
Molecular formula (literature): C5H6N2O
Molecular weight (literature): ~110.11 g/mol
Core scaffold: a six-membered aromatic diazine (pyrimidine) bearing ring nitrogens at positions 1 and 3.
Substituent: a methoxy group (–OCH3) at the C2 position between the two ring nitrogens.
Structural features: planar, π-deficient heteroaromatic; two ring nitrogens (sp2) are strong σ-acceptors and π-acceptors, increasing electrophilicity at C2/C4/C6; methoxy is an electron-donating substituent by resonance but can behave as a leaving group on an activated diazine under SNAr or metal-catalyzed C–O activation.
2D verbal depiction: a pyrimidine ring (positions 1 and 3 = N). At position 2 (between the two nitrogens) is –OCH3; remaining ring atoms are carbon with implicit hydrogens at C4, C5, and C6.
Synthetic Utility
Functional group reactivity
Electron-poor diazine activates ipso positions for SNAr; 2-OMe can act as a leaving group under basic/thermal or catalytic conditions, enabling installation of amines, thiols, alkoxides.
The ring nitrogens direct lithiation at C5 (and sometimes C4/C6) with strong bases at low temperature.
Named/related transformations (informational)
SNAr on diazines (Sanger-type substitutions on activated heteroarenes).
Ni-catalyzed C–O activation cross-couplings (e.g., Kumada/Negishi/Suzuki from aryl methyl ethers using Ni/NHC or Ni/PR3 systems).
Directed ortho-metalation (DoM)-like strategies on azines with LDA/s-BuLi, followed by electrophile trapping (formylation, halogenation, carboxylation).
Retrosynthetic value
2-Methoxy is a traceless activating/handling group: install early (from 2-hydroxypyrimidine via methylation) and exchange late by SNAr to diversify.
Orthogonal derivatization: keep C2 as OMe while introducing handles at C4–C6 (e.g., halogenation, borylation), then perform final C2 substitution.
Practical notes
Dry conditions favor strong-base chemistry; quench carefully to avoid ring N-oxide formation if oxidants are present.
Monitor SNAr by LC–MS to detect demethoxylation or over-alkylation; methanol byproduct can shift equilibria—vent or trap as appropriate.
Target Specificity
Not applicable. This product is a small-molecule heteroaromatic reagent, not an antibody, enzyme, or biological probe with defined target specificity. For biochemical studies, any binding interactions would be context-dependent on derivatives synthesized from this scaffold.
Need help choosing the grade?
Our grade selection guide covers purity, stabilizer status, and application suitability for all variants in our catalog.
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