[panathinaikos13]

Hi I am not very familiar with organic Chemostry but i need to use -COOH in a molecular Dynamic simulation. I am trying to find the geometry in space of COOH and i get two answers. 1st is that all the atoms are at the same plane and 2nd that the H is not at the same. which one is the correct?
Thank you
jim

[Honclbrif]

Do you get energy values for these conformations when you calculate them? If so, which one is the lowest, and what's the difference between them?

[fledarmus]

The carbon and the two oxygens are all in the same plane. The hydrogen is free to rotate in aprotic solvents. In protic solvents, there is usually hydrogen bonding involving one or both oxygens and the hydrogen - since the hydrogen is free to rotate, the nature of the hydrogen bonding usually determines the position of the hydrogen. Even in aprotic solvents, if the carboxylic acid isn't hindered, it will usually form hydrogen bonded pairs rather than being completely solvated.

By "hydrogen free to rotate", of course, I mean there is free rotation about the C-OH bond. The two most stable rotamers are the one where the proton overlaps the C=O bond and the one where it is 180* opposed, but there isn't much of a barrier to rotation so all of the other possibilities are occupied to some extent.

[panathinaikos13]

Thank you for your answer. I am planning to insert these COOH in a nanotube by bonding a C from the Carbonannotube with the C from the COOh. The CNT is very narrow and in first place i would like to keep the COOH rigid. can i put them in the same plane ?

[fledarmus]

Well, the carbon in the nanotube will not react with the COOH. Carbon in a nanotube already has four bonds, in a graphite-sheet like structure. You will not be able to form a bond between that type of carbon atom and your acid. If there was any way to do that, it would form the bond on the outside of the tube (due to relieving the stress of the curved structure)  or at the very end of the tube (where some of the carbons do not already have four bonds to other carbons), not inside.

You can, however, get the molecule containing the acid inside the tube. That would be a very hydrophobic site, and it would probably actually be two carboxylic acid molecules held head-to-head by hydrogen bonding between the carboxylic acid groups, but if the rest of the molecule was long straight alkyl chains, it could probably be done.