(Replying to PARENT post)
And many more do not.
> if you took those molecules and gave massive doses to rats, some may comeback as carcinogenic.
Luckily we don't have to guess. For example, look at the hundreds of terpenoids that saturate traditional diets, many of which and are widely believed to prevent cancer. If you have any actual evidence, put it up.
> The multi ring structure to me suggests...
All this is interesting, but it has exactly nothing to do with in vivo carcinogenicity. You don't have to look far to see this is true. Healthy diets are chock full of polyphenols that exhibit significant DNA binding affinity, but lack evidence of carcinogenicity. And it's not for lack of looking.
You appear to have some specialized knowledge, but when you try to extrapolate it to a wider field where you're out of your depth, these hand-waving guesses can easily turn into fearmongering.
(Replying to PARENT post)
Absolutely, geometry of electric fields is the primary factor in biochemical interactions. "The electron is where its at" as my o-chem teacher always said.
But that's exactly why aspartame is totally different than intercalators like EthBr, doxorubicin, and PAHs. That phenyl moeity has a rotational degree of freedom, and the whole peptide backbone is floppy. EthBr has a Ph but it's stabilized in-plane by the tri-ring. Intercalators typically have 300-500 daltons worth in a "planar greasy brick" regime, with very little in the way of bulky or floppy steric groups. On paper, aspartame looks pretty flat, but you gotta think about thermal molecules in solution.
E: just noticed this
> I would also say two rings with a carbon-carbon link seem to be potent binding as well.
Oh yeah, like biphenylyl, -Ph-Ph? So that's actually much more planar than a single Ph. The conjugation (any time you see carbon chains with alternating double bonds) of the pi-orbitals stabilizes the rings in-plane. Also it's rather unnatural, there's not a lot of reactions which forge a sigma bond between two aromatics like that.
(Replying to PARENT post)
From the purely geometric model, some of the molecules you proposed have pretty large functional groups adjacent to rings which I think may make the intercalation process less efficient. That being said, if you took those molecules and gave massive doses to rats, some may comeback as carcinogenic.
I think that your multi-ring point is fair. The multi ring structure to me suggests that the more the pi orbitals are able to delocalize their electrons the higher the binding efficiency. I have tested 1-2 molecules where non-fused rings showed some affinity but not near the potency of fused ring structures. I would also say two rings with a carbon-carbon link seem to be potent binding as well. I presume that it’s also related to delocalizing pi orbitals and extra degrees of freedom in the intercalation process but I suppose that’s just speculative.