Hey /sci/, I want to do my thesis in determining the mechanism of a catalyzed polymerization using computational methods. More specifically, using QM/MM methods (Quantum Mechanics/Molecular Mechanics hybrid). The problem is that I do not know shit about that, what software to use or if the ones available are reliable.
Do you know any books that describe those methods in detail? What software are the better if there is a good one? I don’t have any problem if I have to learn a new programming language, learn advanced numerical methods or complex quantum chemistry.
Also, chemistry thread
>>8669787
Woah, a fellow computational chemist here on /sci/, rare
QM/MM codes are generally written by the group themselves
Other than that Gaussian, MOLCAS, GAMESS provide good tools for methods like CASSCF and DFT
Frank Neese's ORCA is also a powerful software (my favorite) since it is free
Anyone got some good resources on this kind of subject?
>>8669855
On what language or platform are usually written those codes? and how long would it take? (I consider myself as a good programmer, but I am not an expert)
Thanks for replying
>>8669861
In QM/MM methods or computational chemistry in general?
>>8669855
Would you recommend computational chemistry as a field? I'm currently at a crossroad in my academic career and I'm seriously considering comp chemistry for pharmaceutical research.
Perhaps computational neuroscience, but I'll see.
>>8669903
I am using this book for a starting point.
>>8669898
During my studies, I've dealt with almost all disciplines of chemistry but our main focus was small molecule activation/enzyme mimicking and fluorescence. It is not like organic chemistry for example, where you synthesize a molecule, characterize it and you are done, go publish. You'll have hard tiem publishing results, harder time generating worthwhile ones. he refferees will be very harsh. But when you do, it is very rewarding. Best journal I could publish in was JOC so far.
I wouldn't recommend pharmaceutical aspect of this work. You would just be a desk monkey without any scientific background necessary. You'll just screen 1000s of molecules for their properties. I'll wear you out.
Instead stay in academy and figure out electronic structure details of certain systems giving insight on more general mechanisms. We managed to get a group to synthesize a catalyst we designed after studying a certain dioxygenase enzyme, imitating it's function with just the active site complex/derivative. And its reactivity was controllable through selections of -R group on the substrate, the transition metal cofactor etc.
The gist is, you'll spend alot of time writing trivial unix codes and looking at numbers but when you see a pattern emerging in that excel sheet, it will make you feel like an actual scientist instead of a simple cook in the lab.
>>8670041
Aren't there jobs in industry for computational design of molecules etc.? Like, you get paid to simulate molecular interactions or something.
Also, do you really use excel?
>it will make you feel like an actual scientist instead of a simple cook in the lab
That's my rationale for wanting to be a computational biologist. I'd rather do cool stuff on a computer than spending 8 hours pipetting liquids into eppendorf tubes.
>>8669787
You're gonna have a bad time.
QM/MM methods take a long time to run.
>>8669917
What the fuck is that shit? Read pic related