Thanks Xin Hao for patiently guiding me in the computational stuff again. I managed to learnt most of the basics today and successfully calculated the conformation barriers of cyclohexane and modelled a simple SN2 reaction:
What you see is the end product of the work. The calculation wise involves some complicated algorithms. The simple SN2 reaction didn't work last week, after nearly 1 day of finding the transition state. The reason being that the basis set is given wrongly. Instead of RHF/6-31+G*, I used RHF/6-31G*. The "+" makes a lot of difference as anion is involved in this reaction and we need to introduce a diffusion function to make the calculation works. For cyclohexane, it's not easy too. I had a hard time finding the boat structure as it always slip to the more stable twist form. What I need to do is to fix the dihedral angle to make sure the conformation is eclipsed.
Kinda stress up today, though I have learnt most of the basics. This is because the initial small project given to me was on optimization of oligopeptide structures, something which I don't like. Being a more hardcore organic synthetic guy, I will prefer reactions related projects. My major project was on reactions but that will have to wait till I finish the peptide stuff. Xin Hao told me that I could talk to Prof. Wu on this matter as he can sense my passion in synthetic stuff. He also worked on some Diels Alder reaction stuff. I could probably continue with his work and stuff related. Anything is fine, so long as it's synthesis related.
Tomorrow will be my first lab TA duty. Hope things will go on well. I don't know why but I am not enthusiastic at all. I recalled being so excited in my first TA duty in NUS that I literally jumped around. I guess the reason is probably because it's MC and not synthetic lab.
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