1

How does one recognize lipophilic points, hydrogen bond acceptors and hydrogen bond donors in organic molecules? For example, provided this SMILES instance

O=C1NC(=O)SC1Cc3ccc(OCCN(c2ncccc2)C)cc3

I know it contains 2 lipophilic points, 5 hydrogen bond acceptors and 1 hydrogen bond donor. How can I determine them?

Rosiglitazone 2D image

Rail Suleymanov
  • 131
  • 3
  • 2
    Can you draw a molecular structure from this SMILES, to begin with? I, for one, can't. Human readability was never the primary objective of this format. – Ivan Neretin Feb 15 '17 at 19:55
  • @IvanNeretin, check the updated question, please. This is rosiglitazone (https://en.wikipedia.org/wiki/Rosiglitazone). – Rail Suleymanov Feb 15 '17 at 19:59
  • 1
    Thank you, that's much better. (Not sure if the SMIILES is still needed, BTW.) Now, all hydrogen atoms attached to N or O are hydrogen bond donors, and all N or O atoms with lone pairs are acceptors. – Ivan Neretin Feb 15 '17 at 20:07
  • @IvanNeretin, could you clarify the statement about "lone pairs", please? And one more question: do I get it right that lipophilic atoms are all remaining non-ring atoms that are nor H-bond donors, nor H-bond acceptors? – Rail Suleymanov Feb 15 '17 at 20:14
  • What's unclear about that? As to what constitutes a lipophilic point in your definition, I'm not sure. – Ivan Neretin Feb 16 '17 at 06:07

1 Answers1

2

To identify hydrogen bond donors: Look for a polarized hydrogen (typically bonded to O, N, S) Hydrogen bonds form from the interaction of a partially positively-charged hydrogen and a (partially) negatively-charged atom. Thus, to "donate" a hydrogen for hydrogen bonding, you need a polarized hydrogen. Hydrogens are polarized by being bonded to electronegative elements: in organic molecules that will typically be O, N, or S.

To identify hydrogen bond acceptors: Look for atoms with electron lone pairs, or otherwise partially negatively-charged sites on the molecule. (Typically O, N, S, or halides). To form an interaction with a polarized hydrogen, you need a source of (partial) negative charge, which typically can come from electron lone pairs. The most common species you'll encounter in an organic molecule include O, N, S, or halides (F, Br, Cl, I).

NMJD
  • 673
  • 3
  • 7