normal Ionizable lipid

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3 years 9 months ago #8613 by namit91
Ionizable lipid was created by namit91
I am trying to parametrize a few piperazine derivatives.
e.g. 1,4-Bis(3-(dimethylamino)propyl)piperazine and similar structures that have ethyl, two methyl etc. groups on the terminal nitrogen in place of the hydrogens.

Could someone offer some advise on how to parametrize the ring structure? Should I use three SN0 beads or 2 SN0 and 2SC1.

Also, should I use SN0 or SNa? Tertiary nitrogen have a lone pair that they can use to form hydrogen bond but, I've seen some other structures like PAMAM dendrimers where tertiary nitrogen are parametrized by a N0 bead.

Thank you.

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3 years 9 months ago #8616 by riccardo
Replied by riccardo on topic Ionizable lipid
I think that 2 SN0 beads for the piperazine should suffice. For example, 1,4-Bis(3-aminopropyl)piperazine ( pubchem.ncbi.nlm.nih.gov/compound/81629 ) could be described by 4 beads (2 SN0 beads for the piperazine and 2 regular bead - not sure about the type from the top of my head - for the tails). The best way to validate such a choice is to build a model and compare experimental and computed free energies of transfer. For example, it could be worth to build a model for the compound above because I see from the pubchem page linked above that there's experimental logP data (-1.43 (LogP), Hansch, et al. (1995) ), so you could validate the model by computing the logP, and optimize the bead choices in case of need.


P.S. I don't fully understand the title you gave to this thread :)

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3 years 9 months ago #8617 by namit91
Replied by namit91 on topic Ionizable lipid
Thanks. I'll give it a try.

I'm sorry for the title. I had originally drafted a larger question and forgot to change the title. My lab uses these amines and reacts them with acrylates to form ionizable lipids. The nitrogen on the amine becomes positively charged inside the endosome. We use them for RNA delivery. Next, I am looking to study the entire lipid molecule too.

Best,
Namit

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