July 15, 2024, 06:57:25 PM
Forum Rules: Read This Before Posting


Topic: Boc Rotamers  (Read 15648 times)

0 Members and 1 Guest are viewing this topic.

Offline Cheemistree8889

  • Regular Member
  • ***
  • Posts: 34
  • Mole Snacks: +1/-0
  • Gender: Male
Boc Rotamers
« on: December 30, 2008, 02:32:02 PM »
Hello everyone,

I have question about rotamers...In my research I've come across Boc-rotamers on a pipecolic derivative (it is proline with an additional carbon in the ring)  and I'm a bit unsure about how to explain it.  The rotamers occur because of the obstruction of the carboxylic acid group correct?  By this I mean the Boc group can travel back and forth but cannot rotate 360 degrees because of the acid group ebing in the way.  Am I correct or could anyone explain this a better way.  I've attached the wiki for pipecolic acid.  My derivative is the 4-hydroxy and it is both N-Boc protected and the methyl ester of the acid.  Any tips on explaining this would be appreciated.

http://en.wikipedia.org/wiki/Pipecolic_acid

Also, I have reason to believe this because of VT NMR, the higher temp should an apparent doublet converging to show the true singlet of the Boc protons.

Thanks,
Eric

Offline macman104

  • Retired Staff
  • Sr. Member
  • *
  • Posts: 1644
  • Mole Snacks: +168/-26
  • Gender: Male
Re: Boc Rotamers
« Reply #1 on: December 30, 2008, 03:23:01 PM »
Just to check you have the following structure?  And for the rotation, we are talking about rotating the C-N bond for the boc group correct?

Offline Cheemistree8889

  • Regular Member
  • ***
  • Posts: 34
  • Mole Snacks: +1/-0
  • Gender: Male
Re: Boc Rotamers
« Reply #2 on: December 30, 2008, 03:28:08 PM »
Yes, and yes.  Well there is a two lined pattern at 1.47 ppm, I assume it is the methyl protons.  And when it is heated to ~40 C the singlet is shown (the two lines form one).  Am I interpreting this correctly?

Offline macman104

  • Retired Staff
  • Sr. Member
  • *
  • Posts: 1644
  • Mole Snacks: +168/-26
  • Gender: Male
Re: Boc Rotamers
« Reply #3 on: December 30, 2008, 03:54:04 PM »
It seems to me that makes sense.  I ran some calculations, in my Chem3D, and I found out I can do dihedral conformation calculations.  I've attached the results below:

If you can't tell we are looking at it from the "front" with the two groups pointing towards us.  The acid obviously in the equatorial position of the "chair" conformation.  Pink dots are electron pairs.  Although, I'm not sure why it doesn't include the pair on the carbonyl or the nitrogen...

You can see that there are two local energy minima (one at 25.15 and 29.10 kcal/mol).

The first image, #1, is the higher of the two states, the 2nd image, is the lower energy conformation.  You can see that in the lower image, the carbonyl is facing the other lone pairs of the methyl ester and that in the higher conformation, the lone pairs of the carbamate are now pointing towards the ester, but still can interact with the acid carbonyl.

The highest conformation, I've also attached for reference.  Hope this is helpful in solving your problem!

EDIT:  Wow, images too big, back up in a sec.

Ok, hmm..images are very blurry it seems, hopefully it illustrates the point though.  Also, is there an easy way to remove the colored backgrounds?  That's what happens when I drop it in paint.
« Last Edit: December 30, 2008, 04:06:11 PM by macman104 »

Offline Mitch

  • General Chemist
  • Administrator
  • Sr. Member
  • *
  • Posts: 5298
  • Mole Snacks: +376/-3
  • Gender: Male
  • "I bring you peace." -Mr. Burns
    • Chemistry Blog
Re: Boc Rotamers
« Reply #4 on: December 30, 2008, 04:07:18 PM »
I increased the attachment limit to 10 MBs.
Most Common Suggestions I Make on the Forums.
1. Start by writing a balanced chemical equation.
2. Don't confuse thermodynamic stability with chemical reactivity.
3. Forum Supports LaTex

Offline Cheemistree8889

  • Regular Member
  • ***
  • Posts: 34
  • Mole Snacks: +1/-0
  • Gender: Male
Re: Boc Rotamers
« Reply #5 on: December 30, 2008, 04:11:40 PM »
That is awesome.  What program did you use to do the calculations?  I'm currently writing my undergraduate thesis and those would be perfect to illustrate my point, but obviously I would want to learn how to do them myself.

Thanks,
Eric

Offline Cheemistree8889

  • Regular Member
  • ***
  • Posts: 34
  • Mole Snacks: +1/-0
  • Gender: Male
Re: Boc Rotamers
« Reply #6 on: December 30, 2008, 04:13:16 PM »
I don't think it is the methyl group, it is the rotation of the C-N bond as Macman said before.

Offline azmanam

  • Chemist
  • Sr. Member
  • *
  • Posts: 1416
  • Mole Snacks: +160/-24
  • Mediocrity is a handrail -Charles Louis d'Secondat
Re: Boc Rotamers
« Reply #7 on: December 30, 2008, 04:16:31 PM »
Quote
I would want to learn how to do them myself.

ditto.  does Chem3D do conformational analysis on specific dihedral angles and output a nice energy curve like that?  or did you plot the energy values in excel or something?  What's the procedure for that?
Knowing why you got a question wrong is better than knowing that you got a question right.

Offline macman104

  • Retired Staff
  • Sr. Member
  • *
  • Posts: 1644
  • Mole Snacks: +168/-26
  • Gender: Male
Re: Boc Rotamers
« Reply #8 on: December 30, 2008, 04:25:12 PM »
Quote
I would want to learn how to do them myself.

ditto.  does Chem3D do conformational analysis on specific dihedral angles and output a nice energy curve like that?  or did you plot the energy values in excel or something?  What's the procedure for that?
Indeed, it is all Chem3D.  I just looked did a search in the help pages for "dihedral calculation".

It also supports double angle plots, although I didn't look at how to do that.

Basically, select your bond of interest, and then go to calculations > dihedral driver > single angle plot.  I would perform an energy minimization though first to make sure you have the minimal conformation for the rest of the molecule, or you get really strange looking curves.

It'll give you the curve, and then you can select points and it'll show you the conformation for that point on the energy diagram.  So I just selected the ones of interest and then saved the image for that conformation.

If you don't want to do a search, the go to Help > Get Started > and select the tutorial for the dihedral driver.

Offline macman104

  • Retired Staff
  • Sr. Member
  • *
  • Posts: 1644
  • Mole Snacks: +168/-26
  • Gender: Male
Re: Boc Rotamers
« Reply #9 on: December 30, 2008, 04:26:46 PM »
I increased the attachment limit to 10 MBs.

Oh that's fine, I was trying to keep the images small so I didn't overload the screen with a huge picture.  Can we allow .zip files on here (they currently aren't allowed)?  Basically trying to attach each image separately made for a really long post which is why I combined them.

Offline Mitch

  • General Chemist
  • Administrator
  • Sr. Member
  • *
  • Posts: 5298
  • Mole Snacks: +376/-3
  • Gender: Male
  • "I bring you peace." -Mr. Burns
    • Chemistry Blog
Re: Boc Rotamers
« Reply #10 on: December 30, 2008, 04:35:40 PM »
I increased the attachment limit to 10 MBs.

Oh that's fine, I was trying to keep the images small so I didn't overload the screen with a huge picture.  Can we allow .zip files on here (they currently aren't allowed)?  Basically trying to attach each image separately made for a really long post which is why I combined them.

Done
Most Common Suggestions I Make on the Forums.
1. Start by writing a balanced chemical equation.
2. Don't confuse thermodynamic stability with chemical reactivity.
3. Forum Supports LaTex

Offline playstyles

  • New Member
  • **
  • Posts: 6
  • Mole Snacks: +0/-0
Re: Boc Rotamers
« Reply #11 on: January 13, 2009, 02:51:07 PM »
I did a project on this in my undergrad work well not on this specifically but this came up in N-boc-proline derivatives.

N undergoes a phenomenon called inversion where it can 'flip' its conformation giving two rotomers that are more appropriately referred to as E and Z conformers rather than any cis and trans or other conformational isomers.
In this case it as though the CO2 portion on the boc gets flipped over leaving the rest of the molecule in its orginial place. and the methyl split due a change in chemical environment.

Sponsored Links