I tried the extraction of plants in sonicator bath and I got better results of yields. I would like to know if this technique is harmful for the extracted secondary metabolites of the plants and which are the most sensitive class of compounds.
Undoubtedly that method is the best so far in extracting pyhtochemicals. No harm done (no molecular chain ruptures) to any of known phytochemicals available in the extract except increasing the yield of the extract..
Sonication is also one of the most widely used methods for the extraction of crude drug. But I reckon this is not the methods of choice for the every extraction. Each extraction methods should be chosen according to the compounds of expectation from the extract. Sonication may damage complex compounds such as glycosides present in the extract. So better to use other methods such as maceration, reflux etc.
Sonication is the fastest, easiest and effective method for extraction, and one can control it with respect to time and temperature of the extracting medium. However, degradation can happen especially in plant materials where the cell walls can collapse under sonication conditions. My advise is to check the substrate before and after the experiment using SEM and/or TEM to determine whether it is destroyed or not.
Sonication is a great way to increase extraction efficiency - also because it destroys cells as mentioned above so that the secondary metabolites are released. I am using it for glucosinolate extractions. The sonication itself does not destroy secondary metabolites that easily, but the heat that develops in your extraction liquid might.
I agree with Nicole and some of the other statements above. We use sonication for the extraction of cardiac glycoside and phenolics (phenolic acids, hydroxycinnamic acids and flavonoid glycoside) without detectable degradation.
As mentioned by Nicole, controlling the temperature is definitely important and some ultrasonic baths can heat up your extraction tubes substantially.
Sonication is very useful technique but with some specific tips. One which has to be considered is that is system based on mechanic energy dissipation. As first the transfering medium should be reconsidered as main problem. From matching the system (frequency, power, power/volume ratio, transferring medium - solvent) depends not only efficiency of extraction, but heat conversion also. Sonication can be but not have to be harmful for many secondary metabolites - but which extraction technique isn't. For your purposes - you should compare two techniques and then chose one - which delivers you better parameters - what are those parameters - you have to decide.
I agree with Joanna very much, each technique has its pros and cons and may cause artifacts. Keep an eye open for those too, especially when applying hot extraction fluids. A famous example is the formation of chamazulene during steam destillation of chamomile flowers which gives the essential oil a blue hue.