What is ageing in terms of chemical bonds?

Your question is a little vague, but I think I know what you are getting at. The smoothness you refer to is about biological, chemical, and physical control of oxidation which is impacted from the very beginning, through fermentation, as much as it is by ageing.

For beer, Kunze describes ageing as resulting from oxidation of products from various reactions. Amino acids degrade to aldehydes (carbonyl functional groups). Given time and appropriate conditions, yeast will make use of sugars as well as the aldehydes and turn them into various types of alcohols. These compounds produce flavours ranging from what Kunze describes as bread-like, wet cardboard, and caramel.

For beer, the choice of grains and whatnot, the water chemistry, the physical heat control, etc. determine the type and amount of amino acids and fatty acids that will have to be contended with by the yeast

One reason we ferment is to get the yeast to eliminate the carbonyls we don't want. We age beer and wine to allow further degradation/conversion into the colours, aromas, and flavours we do want. This relies on the physical and environmental conditions (time, oxygen, temperature, water chemistry) as well as the biological conditions (ingredients, yeast, bacteria, fungus etc).

The same goes for wine where oxidation can convert ethanol through a series of reactions to produce acetylaldehydes which impart wonderful colours, aromas, and flavours. We don't want to undo the hard work and time the yeast has already spent scrubbing out the poor-tasting aldehydes by introducing oxygen (airlocks for the win!).