How to effectively use organic solvents in lyophilization

As scientists expand the range of freeze drying applications, they are starting to use organic solvents in lyophilization more frequently. This post attempts to break the ice around using notoriously difficult-to-freeze organic solvents. Read on to see how you can incorporate organic solvents in your laboratory freeze drying workflow without damaging your equipment or your sample.

I was making a right turn the other day and almost rammed my car into a shiny Tesla driving past me. As I pulled up behind the electric car, thanking my lucky stars I am not 100,000€ poorer, I started thinking about how we fuel our cars. For the longest time, gasoline engines have been the most popular option for automobiles. But rising oil prices and environmental concerns have made other methods to power our cars, from electricity to ethanol to fuel cells, gain in popularity. The nature of the human mind to re-invent is blatantly apparent when it comes to the automotive engine.

The same could be said about freeze-dryers. Initially, chemists used laboratory freeze dryers only with water as a solvent. Soon, they realized they need more options. They wanted to lyophilize water-insoluble products. Or even more interesting to me as a lover of chromatography, they wanted to directly freeze dry chromatography products that were not always dissolved in water. So naturally, chemists turned to using organic solvents for laboratory freeze drying.

Using organic solvents can be challenging at first, but it can certainly pay off. The following tips aim to help you successfully adopt organic solvents in your lyophilization workflow.

How to determine if a solvent can be freeze dried

Many organic solvents have a low freezing point, often well below that of the condenser surface temperature. Four key questions can help determine if and how a solvent can be freeze-dried:

How can the solvent be frozen?
Find the most appropriate method that can reach a low enough temperature so that the sample is fully frozen.

At which concentration can the solvent be frozen?
Determine if the solvent must be diluted prior to freezing.

Can the condenser collect the solvent?
The temperature of the condenser must be 15-20°C lower than the freezing temperature of the solvent

Will the sample remain in a frozen phase during the process?
Evaluate if you can maintain a pressure that is low enough to keep the sample frozen.


SolventTtriple [°C]Ptriple [mbar]
Acetone-94.72.33 x 10-2
Methanol-97.71.86 x 10-3
Ethanol-123.154.3 x 10-6

In contrast to aqueous samples, organic solvents are tricky to freeze and require dilution prior to freezing. Chemists might need to use liquid nitrogen for the solvents to reach a low enough temperature. Moreover, due to the low freezing point of organic solvents (see table above), the condenser temperature might not be low enough to completely capture the solvents. Even -105°C condensers can fail at trapping these types of solvents. Instead, the organic solvents liquify in the condenser or leave the system through the pump as vapor. Because of this:

A scroll pump is recommended for all freeze-drying applications involving organic solvents.

The low freezing temperature and triple point of the organic solvents makes it difficult to evacuate the system fast enough and to maintain a low enough pressure to avoid solvent melting, even at ultimate vacuum. For diluted solutions, it is rather common to see solvents melting and evaporating, while water remains frozen. Whether this is problematic for you depends on your sample requirements.

If the solvent amount is too high, the system will not be able to maintain the required pressure and everything will melt and evaporate. The process must be terminated at this point.

Tips on how to handle organic solvents in laboratory freeze dryers

  • Eliminate as much of solvent as possible before freeze-drying, using a rotary evaporator or other instrument
  • Be prepared for periodic replacement of parts when etching of the equipment becomes problematic
  • Carefully cleanse freeze-dryer after each cycle
  • Do not allow condensate to sit in the condenser. Immediately conduct defrosting step of the instrument with the drain valve open. Wash out the condenser with water and ensure it is clean and dry.
  • Use a dry pump when handling solvents other than water. Make sure the exhaust port of the pump is in a fume hood to avoid solvent exposure
  • Use of ultimate vacuum pump is recommended due to the low pressures (lower than 0.05 mbar) required to keep the solvents in solid form
  • Dilute solvents with water whenever possible to influence solvent concentration in your favor

Example of compatibility of common organic solvents with Lyopvapor L-200

The sample can be freeze-dried properly. Sublimation occurs.
The pressure in the drying chamber cannot be set to a low enough value to maintain the solvent in solid form. The solvent will melt while water will remain in ice form. The solvent will evaporate and an increase in pressure can be observed until it is evaporated completely. The ice will then sublimate. Even though the solvent is not sublimating, evaporating it is good enough for many applications.
Solvent100%50%30%10%≤ 5%
Acetic acid
Trifluoroacetic acid

It might be challenging to find a car charging station or bioethanol fuel station, but it might be worth the trouble in the long run. Same with using organic solvents in lyophilization. The ends might just justify the means.

Excited to see if I will discuss chromatography or freeze drying with you next? Stick around to find out.

Till next time,


The Signature of Bart Denoulet at Bart's Blog