How much headspace should I leave when I bottle my beer?
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Answer: This is a question that seems to have generated a lot of controversy in the past. Some brewers claim that proper carbonation will not occur without some headspace, and will overcarbonate with excess headspace. As it turns out, it is not true; it violates the concept of equilibrium thermodynamics. The Homebrew Digest back in 1996 describes some experiments run by Steve Alexander and Al Korzonas that prove this out. Check out http://hbd.org/hbd/archive/1938.html#1938-17 for example. As long as the beer still has some viable yeast, carbonation depends mainly on the amount of priming sugar, not on the headspace. Bottles with extra headspace will reach full carbonation faster, however. This is because the extra oxygen in the headspace allows the yeast a brief reproductive phase.
Despite these fairly well run experiments, people expect quite a bit of headspace. This is particularly evident in competitions, where up to 1½ inches is commonly allowed. In part, this may be due to the fact that most of the bottle fillers on the market leave extra room when they are pulled out of the bottle.
In my opinion, 1½ inches is way too much. Generally, good brewing practice calls for minimizing oxygenation during bottling, so you ought to keep the fill level high. . Any oxygen not consumed by the yeast will go into unwanted oxidation processes. These can degrade the malt flavor, resulting in a cardboard-like flavor, and can degrade hop aroma. The greatest risk in underfilling bottles is the risk of developing acetaldehyde. Acetaldehyde is the result of direct oxidation of ethanol, and has a foul solvent-like aroma and flavor that can make an otherwise good beer undrinkable. Acetaldehyde will invariably form if the fill level is below the shoulder of the bottle. Another risk of underfilling relates to bottle detonation. If the beer is incompletely fermented or overprimed, the bottles are much more prone to dangerous fragmentation.
If your filler leaves too much headspace, you ought to top it up before capping. Another trick is to leave the caps loose for half an hour or so. As CO2 escapes from the beer it will tend to flush oxygen out.
So, should you fill the bottle all the way up to the brim? No, since beer expands when allowed to warm up. Expanding beer creates unimaginable pressure (far more than overpriming) that will either break bottles, or at least will cause leakage out of the cap. The amount of expansion will depend on how stable you keep your storage temperature. Don't forget to add a bit for unexpected heat, such as leaving beer in your car, for example. I had one nasty experience where a bottle burst all over the floor of my car. Wow, what a stink!
I personally fill my bottles quite high. However, I've often gotten comments
about high fills in competition even if I've left a half an inch. Thermal expansion
requires about 1/8" (1/4" for 22 oz bottles) so I try to keep the
fill between ¼" and ½".