Yesterday I just had the calculation running to keep me entertained while I was studying for biochemistry. I guess I shouldn't have posted the picture without checking it right away. Here's the redone version. The structure was optimised with semiempirical quantum mechanics (PM3) in Arguslab.
What was wrong?
The nitrogens should not have hydrogens bonded to them. It is a problem with the delocalised bonds. If you separate them into single and double bonds the situation would be obvious. I needed the resonance structures for molecular mechanics, in order for all bonds to be the same length.
A hydrogen was missing at the 5'-C, no idea why.
The third thing I think was wrong is the amino nitrogen. It may have been too pyramidal because classical MM can't properly include conjugation effects. I don't know if it should be all the way planar or a little bit bent. The structure depends on the semiempirical method used (AM1 makes it planar, PM3 and MNDO bent). I guess I would need an ab initio calculation to do that. But I don't have a computer program and I don't have 64 parallel chips working for me. Í have to ask my professor if I can get access to our school's Gaussian. That would be amazing. But I don't know if it would work. Another problem is that I modelled an isolated gasphase molecule at absolute zero (something you don't have a lot in real life).
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