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Attach Methyl with DNA


I want to attach methyl forming covalent bond with Oxygen of Guanine in DNA. How can we do it using Avogadro ?



I’m not 100% sure what you want, but let me take a stab at it.

So you want to change the C=O to a C-O-CH3 to add the methyl at the end?

The big question is what happens to that ring C atom. I’m not sure what you want to do there.

But you can click on the C=O bond to change the bond order. It will cycle to a triple bond and then another click will make it a C-O bond. By default, you’ll get a hydrogen buried somewhere in there, and a O-H terminus.

Note that weird H buried inside the O… As I said, I have no idea what you want to do with the ring carbon atom (e.g., where you’d want to put that hydrogen).

You can then click on the H atom at the end of the O-H bond and it will (by default) change to a methyl:

You’ll still need to figure out what to do with the buried hydrogen…