> I think a geometric interpretation can help some non-chemists understand how intercalating molecules bind to dna.
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.
If it's fully unsaturated, 1,4-oxazinane. If it's 2 double bonds, 1,4-oxazine, or more commonly oxazinone if it's part of a larger fused structure (eg nile red). If you fully aromatize it, it becomes oxazinium. That's a weird one, probably unstable. I think there are some peroxo species with a 1,4-oxazin-1-ium but it's a bit wacky.
The meta (1,3) oxazinium is more stable, but it still needs 3 big electron-withdrawing groups to stabilize it in the case of 2,4,6-Triphenyl-1,3-oxazine-1-ium.
Thank you. I was looking at a vermicide that had what looked like a complicated nitrogen cage, empty, with a pair of those hanging off, and I realized I had no idea what to call them.
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.
https://en.m.wikipedia.org/wiki/Biphenyl