New answers tagged computational-chemistry
6
You're describing simple Hückel theory. This is usually applied to $\pi$-conjugated systems to understand the stabilization in conjugated and aromatic molecules.
There are a variety of Python packages, for example:
Felix Plasser wrote one for his blog and the current location is at his homepage
Randle Taylor has a SHMO package on GitHub, including a GUI ...
1
It's not an all-or-nothing situation, where either we can reliably prediction reaction products, or we have not tried to.
For instance, drug companies, for many years, have been making extensive use of increasingly powerful, sophisticated, and refined in silico predictive models to choose likely candidates for in vitro testing. And I would be surprised ...
0
Only the program that you used to calculate the electronic structure knows all the idiosyncrasies of the computation to correctly evaluate the orbitals. Therefore, what most people do is to export the evaluation of the orbitals in a grid. Then, a plotting program performs an extraction of a polygonal mesh with a marching cubes (or similar) algorithm.
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I don't know about that particular GitHub archive, although I'll point out that the smiles.csv contains several kinds of SMILES - the final column containing the correct SMILES.
IMHO, this is an unfortunate result of people mis-using SMILES. As you note, it's perfectly possible to take a chiral molecular structure and output a SMILES with no stereochemical ...
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As several comments have mentioned, interpreting a machine learning method can often be difficult. Outside the question of machine learning, I think your question centers around "what would I want to know to roughly predict HOMO / LUMO energies?"
Unfortunately QM9 isn't very diverse chemically, but if we think from a general qualitative molecular orbital ...
3
This is the way of directing the electrophiles to the ortho and para places of the benzene cycle. As you see the ortho and para places are more negatively charged.That's true. It is due to the ability to donate its electron pair to the benzene cycle.
But an electronegative element can attract the electron cloud to it. Fluorine is the most electonegative ...
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