Solvent Etiquette¶
Introduction¶
Solvents are a shared resource in the lab. Proper management ensures that everyone has what they need and that we maintain a safe working environment. This page covers ordering guidelines, storage, and safety considerations for the solvents we use most frequently.
Etiquette Rules¶
- Check before you start. If a solvent bottle is getting low, check whether there is a backup. If not, order more before you run out.
- Replace what you use. If you empty a bottle, replace it or notify the person responsible for ordering.
- Label everything. If you transfer solvent to a secondary container, label it clearly with the solvent name and date.
- Keep the solvent area clean. Wipe up spills immediately and return bottles to their designated locations.
- Close caps tightly. Solvents evaporate and absorb moisture. Always close caps tightly after use.
When to Order More¶
Table 1: Heavy-Use Solvents¶
These solvents are consumed rapidly. Order more when you open the last bottle.
| Solvent | Common Uses | Container Size | Typical Stock |
|---|---|---|---|
| Acetonitrile (ACN) | HPLC, reactions, PAMPA | 4L | 2-3 bottles |
| Dichloromethane (DCM) | SPPS washes, extractions, column chromatography | 4L | 3-4 bottles |
| Acetone | Glassware rinsing, cleaning | 4L | 1-2 bottles |
| Dimethylformamide (DMF) | SPPS coupling, Fmoc deprotection | 4L | 2-3 bottles |
| Ethyl Acetate (EtOAc) | Extractions, column chromatography | 4L | 2-3 bottles |
| Hexanes | Column chromatography, precipitation | 4L | 2-3 bottles |
| Methanol (MeOH) | LC-MS, extractions, cleaning | 4L | 2-3 bottles |
| Isopropanol (iPrOH) | Cleaning, quenching | 4L | 1-2 bottles |
Table 2: Other Solvents¶
These solvents are used less frequently. Order more when you are down to the last bottle.
| Solvent | Common Uses | Container Size | Typical Stock |
|---|---|---|---|
| Toluene | Azeotropic drying, reflux reactions | 2.5L | 1 bottle |
| Diethyl Ether (Et2O) | Extractions, washes | 4L | 1 bottle |
| THF | Reactions, Mitsunobu, N-alkylation | 4L | 1 bottle |
| DMSO | Stock solutions, reconstitution | 1L | 1 bottle |
| Pyridine | Base, solvent for reactions | 500mL | 1 bottle |
| NMP | SPPS, oNBS removal | 1L | 1 bottle |
| 1,4-Dioxane | HCl/Dioxane for Boc removal | 1L | 1 bottle |
| Piperidine | Fmoc deprotection | 500mL | 1 bottle |
| HFIP | Resin cleavage | 100mL | 1 bottle |
| TFA | Global deprotection, Boc removal | 100mL | 1 bottle |
Solvent Notes¶
Acetonitrile (ACN)¶
ACN is used as the organic mobile phase for LC-MS and as a solvent for many reactions including DSC couplings. HPLC-grade ACN should be used for analytical work. Reagent-grade ACN is fine for reactions.
Dichloromethane (DCM)¶
DCM is one of the most heavily used solvents in the lab, primarily for SPPS resin washes, extractions, and column chromatography. DCM is denser than water. It is a suspected carcinogen -- use in the fume hood and avoid skin contact.
Acetone¶
Acetone is used primarily for rinsing glassware. It is also used to clean the Prelude synthesizer bottles after a run. Do not use acetone for reactions unless the protocol specifically calls for it.
Dimethylformamide (DMF)¶
DMF is used extensively in SPPS for coupling reactions and Fmoc deprotection. DMF is a reproductive toxin -- avoid skin contact and inhalation. Use peptide-synthesis-grade DMF when possible, as reagent-grade DMF can contain dimethylamine which interferes with Fmoc chemistry.
Ethyl Acetate (EtOAc)¶
EtOAc is used for extractions and column chromatography. It is less dense than water. EtOAc is a relatively benign solvent but is flammable.
Hexanes¶
Hexanes are used for column chromatography (with EtOAc) and for precipitation of products. Hexanes are flammable and should be used in the fume hood.
Methanol (MeOH)¶
MeOH is used for LC-MS, extractions, resin capping, and cleaning. MeOH is toxic -- avoid inhalation and skin contact. Use HPLC-grade for analytical work.
Isopropanol (iPrOH)¶
iPrOH is used for quenching sodium hydride, cleaning, and some reactions. It is a relatively safe solvent but is flammable.
Ethereal Solvents¶
Peroxide Formation Hazard
Ethereal solvents (diethyl ether, THF, 1,4-dioxane) can form explosive peroxides upon prolonged exposure to air and light. Never distill an ethereal solvent to dryness without first testing for peroxides. Check the date on the bottle -- if it has been open for more than 6 months, test for peroxides before use.
Diethyl Ether Safety
Diethyl ether is extremely flammable with a very low flash point (-45 C). It is denser than air and vapors can travel along bench tops to ignition sources. Always use diethyl ether in the fume hood, away from any open flames or hot plates. Never store large quantities of diethyl ether on the bench.
THF Safety
THF is a peroxide-forming solvent. It is also flammable. Use THF in the fume hood. Dry THF should be obtained from the solvent purification system when anhydrous conditions are required. Store THF with BHT inhibitor when not using anhydrous grade.