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I notice that professionals tend to always melt chocolate in a basin over steam to prevent burning. I have over time become lazy and melt chocolate in the microwave on defrost as this is SOO easy also doesn't burn it. But I am wondering if the act of microwaving it would interfere with the structure of the chocolate?

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When you say "structure" do you mean that you're trying to melt the chocolate but leave it tempered? Or are you just doing things like stirring the chocolate into baked goods, in which case you're not really using any structural properties of it at all? – Jefromi Aug 1 '12 at 0:24

If all you're trying to do is melt it, then there's no structure you can mess up. The only harm you can cause is by scorching or burning spots, which might happen if your microwave is uneven and you heat too fast without stirring. But otherwise, the microwave is a great way to melt chocolate. Open it up and give it a stir now and then, be careful not to overheat (sounds like you are), and you'll be fine!

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It very well might destroy the structure of the chocolate. Since cocoa butter has a crystalline structure, when it cools it will set differently based on how how it was.

If melt chocolate over water, you're guaranteed (more or less) that none of it will reach a temperature over 212 Fahrenheit. If you melt it in the microwave, due to the nature of the microwave, there might be spots well over the boiling point, and spots that are well under the boiling point. It won't be burned, but when it cools, you might not get the uniform texture that you're guaranteed to get using a double boiler.

See below on how temperature affects chocolate texture:

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As the wikipedia article you linked says, all of the crystals melt by 45°C (113°F), so it's quite easy to get rid of all the structure in a double boiler too. And it's not completely clear, but it doesn't sound to me like the OP is really trying to temper her chocolate anyway, so given that she's using the microwave on a low setting, and can easily stir it at the end, I doubt your concerns apply to her. – Jefromi Aug 1 '12 at 0:33
Yes I am not at this stage trying to temper chocolate. That looks far to complicated and fiddly to do in my small kitchen. – Ellie Aug 1 '12 at 0:41

I Agree with Jefromi. However, if you are also talking about the structure of the chocolate crystals, you might want to stir in some well tempered chocolate after you melted the chocolate. In this way you add 'good crystals' to your melted chocolate to improve the crystal structure.

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Yes, if you intend to retemper overheated chocolate, seed crystals are good. But an important point is to only use them while the chocolate is in the tempering stage, not above or below. – rumtscho Aug 1 '12 at 7:34

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