Nomenclature of carbohydrates - (Dec/07/2011 )
Hi all,
I have some questions about the 'ring' structures. Please look at
http://en.wikipedia.org/wiki/Fructose_1,6-bisphosphate
and
http://en.wikipedia.org/wiki/Fructose_2,6-bisphosphate
Where do you find all carbons, is simply every corner a carbon atom?
If so, what carbon is the "first" carbon? In Fructose 1,6-bisP they count from right to left, while on the 2,6 version they count from left to right if I'm not mistaken.
I mean, why is it 2,6-bisphosphate and not 1,5-bisphosphate?
And what does the --==|||||| shaped bounds shown in the picture actually mean?
I can't realy find a good answer to these questions. Can anyone provide me with some information about this matter?
Greetings,
Rob
take a look at the wikipages , but the dutch ones (I think you speak dutch?) Then you might understand where the 1, 6 and 1, 2 come from?
THey start counting at the right right, starting from the first C (the CH2OH)
And the "dashed" lines ("het zeprapad") means the molecule is "above" the "central molecule" , while the full line means its underneath the central molecule.
I hope you understand wht I mean?
Yes I am Dutch, I looked at the pages like you told me to. I already figured out where they started counting, I just don't understand why they start counting at that position rather than on other side, which would give 1,5 instead of 2,6.
About the dashed lines, what exactly do you mean by "above" and what exactly is the 'central molecule'?
Thanks for the help!
Greetings,
Rob
robvleugel on Wed Dec 7 21:15:16 2011 said:
Yes I am Dutch, I looked at the pages like you told me to. I already figured out where they started counting, I just don't understand why they start counting at that position rather than on other side, which would give 1,5 instead of 2,6.
About the dashed lines, what exactly do you mean by "above" and what exactly is the 'central molecule'?
Thanks for the help!
Greetings,
Rob
check the dutch website... do you see where you find dashed lines and where "full" lines?
If the molecule is above the central "sugar molecule" they use a dashed line... if its below the central molecule its a full line...
(in dutch: de centrale molecule is de "suikermolecule" , die met de C's rond de O, en kijk naar waar de fosforgroepen liggen in vergelijking met de ringstructuur... erboven of eronder... en kijk nu naar de gestreepte lijn en de volle lijn.. je zal zien dat de volle lijn gebruikt wordt als de fosforgroep boven de ringstructuur ligt en de volle als het eronder ligt..gebruik de nederlandse wiki voor de tekeningen te zien, daar is duidelijk aanegeven of de OH groepen of fosforgroepen boven of onder liggen.)
And why they start counting there? Its just an agreement (I think, not sure really... but there is no real reason to start counting on the left/right/middle...)
It's confusing because the 2,6 bisphosphate diagram is turned upside down and left/right reversed. Position 1 is defined as the start of the chain leading to the smallest numbered modifications to the chain. Position 2 has both a hydroxy modification and a link to the ring oxygen. Position 5, on the other hand, has only the ring oxygen. They conveniently left off the numbers, to further your confusion. If you're motivated, perhaps you could fix the diagram by putting it in the same orientation and adding numbers.
I have a doubt on the counting part
..is this not because in nomenclature the priority is given to hydroxyl group that should be in plane. What I mean here is, if you see structure of 1,6 bisphosphate...then according to this counting hydroxyl group that is in plane comes at 3rd position whereas if you count from the other side, it will come at 4th position that is why first one is preferred
....same with 2,6 bisphosphate...I may be wrong, this was just an observation.....Just wanted to confirm can this be a reason too??
phage434 on Thu Dec 8 02:43:25 2011 said:
It's confusing because the 2,6 bisphosphate diagram is turned upside down and left/right reversed. Position 1 is defined as the start of the chain leading to the smallest numbered modifications to the chain. Position 2 has both a hydroxy modification and a link to the ring oxygen. Position 5, on the other hand, has only the ring oxygen. They conveniently left off the numbers, to further your confusion. If you're motivated, perhaps you could fix the diagram by putting it in the same orientation and adding numbers.
I have never heard of that rule...
I was always told that it doesnt matter: you either start counting from the left or right and start at the first carbon.. (and most start at the right).
Anyway, the following links might help you understand how it works.
http://www.chemguide.co.uk/basicorg/conventions/names.html (here you see how the counting works and why sometimes molecules are "reversed or upside down" )
http://www.chemguide.co.uk/basicorg/conventions/draw.html#top (check this for your question about the dashed lines and full lines..)
Well, consider the molecule 2-methyl pentane. If you could start numbering at either end, then it might also be called 4-methyl pentane. This would make it difficult to realize it was the same molecule (of course non-systematic names make this a problem in any case). SMILES descriptions are pretty good.
phage434 on Thu Dec 8 15:14:44 2011 said:
Well, consider the molecule 2-methyl pentane. If you could start numbering at either end, then it might also be called 4-methyl pentane. This would make it difficult to realize it was the same molecule (of course non-systematic names make this a problem in any case). SMILES descriptions are pretty good.
I see your point, however I have learned that 2-methyl pentane is indeed the same as 4-methyl pentane
Take for example
Here's a reasonably coherent set of the rules. The alternative to your example is 5-bromo-2-methylpentane, which has higher numbers, so your version is correct.
http://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistry