pstjohn / bde Goto Github PK

Hello,

Is "type_ == "fragment"" referring to the molecule which is a RADICAL species? The reason that I asked is because when I looked at fragment.py file, to me, "fragment" is defined to be a species with an undefined stereochemistry; however, I am unsure whether my understand is correct.

Furthermore, may I ask a difference between gaussian.py vs guassian_crest.py? Both of them will first optimize and find the minimum energy conformer and run gaussian but I cannot spot a difference between them besides running crest before gaussian in gaussain_crest.py.

Hello, awesome project here!

I'm a complete beginner when it comes to quantum computational chemistry, but I'm interested in predicting spectra of organic molecules and so was excited come across your paper and this project. I was able to successfully download the data from figshare and load it as a dataframe following the first 5 cells of your notebook. When I look at IRIntensity and VibFreqs though it seems like the length of these vectors varies for each molecule and in ways that I don't understand. Naively I was expecting VibFreqs to range over some fixed interval (and be the same for every molecule!) and then IRIntensity report the IR absorption at each frequency. I was hoping to make spectral plots like the following

but it is now clear to me that I don't really understand what information is in VibFreqs and IRIntensity. Should I take the unspecified values to be zero and then do some smoothing? Or am I way off with what these data represent. Apologies if that is a really dumb question. If you could you give me any pointers on how I could make plots of the IR absorption spectra though that would be great. Maybe also any additional information on how you used Gaussian to predict the IRIntensity would be helpful too.

Thanks so much!!