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Topic: What is this structure?  (Read 14347 times)

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Offline Kikko

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Re: What is this structure?
« Reply #15 on: June 03, 2013, 05:08:32 AM »
After reading the list provided, I'm thinking it could be hemiaminal, but that has 5 R groups.  Is it a hemiaminal?

The specific linkage in the red box is a hemiaminal - not sure where you are getting 5 R groups from:

You have in this case:
[*:1]OC([*:2])N[*:3]

R1 = sugar ring; R2 = sugar ring; R3 = Asn residue of peptide

More specifically (also considering what is outside the red box) you could call this structure an N-acyl hemiaminal (because R3 is an acyl group).

Based on the core amide structure:

[*:1]NC(=O)[*:2]

and given that R1 = glycosyl, you could call it an N-glycosyl amide. There are a lot of functional groups present, so there is more than one logical way of describing what is present.

In the PDF file you posted, with the names, there are 5 R groups, I guess thats why he is confused that its an hemiaminal.

On wiki its showing an "easier" structure:
http://en.wikipedia.org/wiki/Hemiaminal


Mod edit: Image resized. Dan
« Last Edit: June 03, 2013, 06:28:42 AM by Dan »

Offline Studentofstuff123

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Re: What is this structure?
« Reply #16 on: June 03, 2013, 05:25:07 AM »
After reading the list provided, I'm thinking it could be hemiaminal, but that has 5 R groups.  Is it a hemiaminal?

The specific linkage in the red box is a hemiaminal - not sure where you are getting 5 R groups from:

You have in this case:
[*:1]OC([*:2])N[*:3]

R1 = sugar ring; R2 = sugar ring; R3 = Asn residue of peptide

More specifically (also considering what is outside the red box) you could call this structure an N-acyl hemiaminal (because R3 is an acyl group).

Based on the core amide structure:

[*:1]NC(=O)[*:2]

and given that R1 = glycosyl, you could call it an N-glycosyl amide. There are a lot of functional groups present, so there is more than one logical way of describing what is present.

Hmmm...thank you Dan.  I will tell my professor on Monday. I am sure he will ask me how I figured it and will definitley tell him from here because he is way too smart to think I figured this by myself. 

He basically challenged everyone in the class to find this and he said NO one has EVER figured it out in 10+ years. I just wanted to see why that was.

I will keep you all posted, thank you.

Offline Kikko

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Re: What is this structure?
« Reply #17 on: June 03, 2013, 05:26:01 AM »
Is it a tertiary amine ?

No, look it up: example of a list I found on google.

In your original post you highlighted this fragment:

[*:1]OC([*:2])N[*:3]

Looking back at it, I am not sure where you get your "fragment".
I can understand the R3 group.
But what is R1 and R2 ? One of them has to be the sugar group where N is linked to (and contains the "red O", but the other R?
Isnt Arkcon his figure better?
=>
OK, so ... removing all the rest of the graphic, and drawing it out, (and converting to SMILES so it displays here,)

CNCOC

Is that sort of close to it -- ignoring that the rest of the sugar ring has to be called a CH3 (I'm not very good at SMILES yet)?  Like everyone else, I see a couple of functional groups, but I don't know a name for this one by itself.  Unless the letters for the atoms spell your school's initials, or something.  Could that be it?

Also
@OP, You must make an attempt; that is a forum rule.  However, I will give you a hint.  The functional group that connects a base (purine or pyrimidine) to a ribose or deoxyribose in RNA or DNA respectively, is similar.
And I dont think the functional group that connects a base to a ribose is an hemiaminal

Offline Dan

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Re: What is this structure?
« Reply #18 on: June 03, 2013, 06:33:19 AM »
Looking back at it, I am not sure where you get your "fragment".
I can understand the R3 group.
But what is R1 and R2 ? One of them has to be the sugar group where N is linked to (and contains the "red O", but the other R?
Isnt Arkcon his figure better?

This is what I did:
My research: Google Scholar and Researchgate

Offline Kikko

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Re: What is this structure?
« Reply #19 on: June 03, 2013, 07:18:02 AM »
Looking back at it, I am not sure where you get your "fragment".
I can understand the R3 group.
But what is R1 and R2 ? One of them has to be the sugar group where N is linked to (and contains the "red O", but the other R?
Isnt Arkcon his figure better?

This is what I did:

Ok, I see what you did, but I am still confused about what R1 and R2 is.
Does R2 refer to the "second" sugar ? (the one attached to the "first" sugar that contains the O that is found in the red square?)

Offline Arkcon

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Re: What is this structure?
« Reply #20 on: June 03, 2013, 07:43:54 AM »
Well, R1 and R2 are by definition anything, since the O.P. drew a red box to exclude much of the ring.  Its a bit confusing, since in the original molecule, what ends up as R1 and R2 are parts of the same ring, but the question isn't about that.
Hey, I'm not judging.  I just like to shoot straight.  I'm a man of science.

Offline Kikko

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Re: What is this structure?
« Reply #21 on: June 03, 2013, 07:48:31 AM »
Well, R1 and R2 are by definition anything, since the O.P. drew a red box to exclude much of the ring.  Its a bit confusing, since in the original molecule, what ends up as R1 and R2 are parts of the same ring, but the question isn't about that.

Ok, but if I look at your drawing compared to the one Dan does.. to me those are different molecules...
Thus changing the name of the functional group?
Or?

Offline Arkcon

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Re: What is this structure?
« Reply #22 on: June 03, 2013, 07:59:26 AM »
Oh yes, 'cause mine is wrong, and doesn't describe the OP's question, I'm new to SMILES.
Hey, I'm not judging.  I just like to shoot straight.  I'm a man of science.

Offline AWK

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Re: What is this structure?
« Reply #23 on: June 03, 2013, 08:19:20 AM »
AWK

Offline Babcock_Hall

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Re: What is this structure?
« Reply #24 on: June 03, 2013, 09:17:39 AM »
It is common to refer to the linkage between a base and the (deoxy)ribose in RNA or DNA as an N-glycoside.  However, this is frowned upon in some circles.  "...however the use of 'N-glycoside', although widespread in biochemical literature, is improper and not recommended here ('glycosylamine' is a perfectly acceptable term)."  One wonders whether the present group might be called a glycosylamide.  http://www.chem.qmul.ac.uk/iupac/2carb/33.html

Offline Kikko

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Re: What is this structure?
« Reply #25 on: June 03, 2013, 10:32:53 AM »
It is common to refer to the linkage between a base and the (deoxy)ribose in RNA or DNA as an N-glycoside.  However, this is frowned upon in some circles.  "...however the use of 'N-glycoside', although widespread in biochemical literature, is improper and not recommended here ('glycosylamine' is a perfectly acceptable term)."  One wonders whether the present group might be called a glycosylamide.  http://www.chem.qmul.ac.uk/iupac/2carb/33.html

Its getting a bit more complicated..

Now how do you call the structure in DNA that you described: @OP, You must make an attempt; that is a forum rule.  However, I will give you a hint.  The functional group that connects a base (purine or pyrimidine) to a ribose or deoxyribose in RNA or DNA respectively, is similar.

You would say its a hemiaminal or glycosylamide ?

 Because I justed asked around and they told me that what you describe is also called a tertiary amine...
So I am confused!

ALso: if I look up the definition of Glycosidic bond, I see it refers to having a hemiacetal group and this is not the case in DNA so I wonder where they came up with this glycosidic bond.

Offline Dan

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Re: What is this structure?
« Reply #26 on: June 03, 2013, 11:47:48 AM »
N-Acetylhemiaminal and N-glycosylamide are both, in my opinion, perfectly acceptable descriptions of the functional group (as I already said in reply #14).

They differ in their level of generality. N-Glycosylamides are a type of N-acetylhemiaminal.
My research: Google Scholar and Researchgate

Offline Babcock_Hall

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Re: What is this structure?
« Reply #27 on: June 03, 2013, 02:08:31 PM »
ALso: if I look up the definition of Glycosidic bond, I see it refers to having a hemiacetal group and this is not the case in DNA so I wonder where they came up with this glycosidic bond.
Glycosides are a form of acetal, not hemiacetal.

Offline Studentofstuff123

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Re: What is this structure?
« Reply #28 on: June 05, 2013, 07:11:46 AM »
He confirmed that it was indeed correct, hemiaminal ether more specifically

Offline Kikko

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Re: What is this structure?
« Reply #29 on: June 06, 2013, 05:26:17 AM »
He confirmed that it was indeed correct, hemiaminal ether more specifically

Pretty weird that the biochemistry majors dont know this.
Altough, I guess its more a thing for (organic) chemistry majors.

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