New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Really confusing NMR for hERG evador: carboxylic acid proton coupled to a triplet??? #451

Closed
ghost opened this Issue Oct 23, 2016 · 8 comments

Comments

Projects
None yet
3 participants
@ghost

ghost commented Oct 23, 2016

For the past three weeks, we have been trying to synthesize our target, the hERG evador, by adding tropic acid dianion, deprotonated by a strong base, to the triazopyrazine core by SNAr reaction:
image

In four reactions in total, the bases we have tried are LDA and NaH. Both bases yield the same compound, but the identity of the compound really confuses us. Identification of the product will help us understand what really is going on and why this SNAr reaction is not yielding desired product, so that we can move forward. We would appreciate any help!

The compound appears to have no tropic acid moiety (6), so it is from (5) alone. It dissolves completely in water (vs THF) at pH 14 (brown color), and have a higher affinity to THF (vs water) at pH 1 (yellow color). At pH 1, it does not dissolve completely in anything but DMSO. The H1 NMR (pH 1-2) is:
full

Partial magnification of aromatic region:
partial

What really confuses us is that, the acidic proton here (~11.5 ppm) seems to be coupled to a triplet, and the triplet is then coupled to something else. COSY here:
For the acidic proton:
acid

For the aromatic region:
aromatic

We feel really thrown off by the fact that the acidic proton (~11.5 ppm) is coupled to a triplet (~11.5 ppm), and the triplet is also coupled to an unidentifiable peak in the cluster of 3 protons (the other two are probably those on the benzene ring). We would appreciate any help!

@mattodd

This comment has been minimized.

Show comment
Hide comment
@mattodd

mattodd Oct 23, 2016

Member

Nice data, good question. First thought - based on some history of us seeing this compound - is it the compound where the Cl has been replaced by an OH? The triplet arising from the proton at position 1 (in your numbering above) that is coupling to the other Ar proton and the OH, where the coupling constants happen to be the same? Not the most convincing explanation, but perhaps the most likely byproduct. @alintheopen @edwintse I think we have NMR data for this compound from @JoannaUbels ? (Jo's experiments are here, though I'm not sure we ever uploaded the thesis, e.g. to Figshare?).

Is this product the major product in call cases? Are you seeing generally good conversion of S/M? Do we think that this nucleophile is just not playing ball (through internal cyclisation @alintheopen ?)

Member

mattodd commented Oct 23, 2016

Nice data, good question. First thought - based on some history of us seeing this compound - is it the compound where the Cl has been replaced by an OH? The triplet arising from the proton at position 1 (in your numbering above) that is coupling to the other Ar proton and the OH, where the coupling constants happen to be the same? Not the most convincing explanation, but perhaps the most likely byproduct. @alintheopen @edwintse I think we have NMR data for this compound from @JoannaUbels ? (Jo's experiments are here, though I'm not sure we ever uploaded the thesis, e.g. to Figshare?).

Is this product the major product in call cases? Are you seeing generally good conversion of S/M? Do we think that this nucleophile is just not playing ball (through internal cyclisation @alintheopen ?)

@mattodd

This comment has been minimized.

Show comment
Hide comment
@mattodd
Member

mattodd commented Oct 23, 2016

@PatrickThomson

This comment has been minimized.

Show comment
Hide comment
@PatrickThomson

PatrickThomson Oct 23, 2016

I had a quick poke around in the literature to see if there were analagous systems we could compare NMR to, but with the exception of one hydroxypyrazine (compound 32, aromatic peaks at 7.72 and 8.08) there was nothing. I checked any potential "keto" form of the hydroxide to no avail.

For routes to the proposed hydroxide, the most obvious is traces of moisture in the reaction mixture, but I also looked for potential decarboxylative routes to the proposed hydroxide plus styrene, (nothing). What did have promise was an internal cyclisation to the 4-membered lactam with the "phenol" as a byproduct, something like:

image

There's literature precedent for a mitsunobu-type reaction generating the lactam efficiently at -78.

I couldn't find any literature precedent for the use of tropic acid dianion as a nucleophile but there must be; it seems unlikely that nobody's come across this before.

PatrickThomson commented Oct 23, 2016

I had a quick poke around in the literature to see if there were analagous systems we could compare NMR to, but with the exception of one hydroxypyrazine (compound 32, aromatic peaks at 7.72 and 8.08) there was nothing. I checked any potential "keto" form of the hydroxide to no avail.

For routes to the proposed hydroxide, the most obvious is traces of moisture in the reaction mixture, but I also looked for potential decarboxylative routes to the proposed hydroxide plus styrene, (nothing). What did have promise was an internal cyclisation to the 4-membered lactam with the "phenol" as a byproduct, something like:

image

There's literature precedent for a mitsunobu-type reaction generating the lactam efficiently at -78.

I couldn't find any literature precedent for the use of tropic acid dianion as a nucleophile but there must be; it seems unlikely that nobody's come across this before.

@ghost

This comment has been minimized.

Show comment
Hide comment
@ghost

ghost Oct 23, 2016

@PatrickThomson @mattodd Thanks! Internal cyclization could explain why tropic acid is not added to the triazolopyrazine ring, and we are having a "phenol". We generated a 1H NMR spectrum for the phenol:
screen shot 2016-10-23 at 12 21 58 pm

The peak ~ 11.5 ppm appears to match, and the integration of protons is correct! I think this is what we have made. It did not occur to us that 1 H NMR shift of a phenol can be so downfield!

The reaction, as it happened, should be pretty dry. We carefully dried all glassware in oven prior to reaction; precursor (5) was dried in high vacuum overnight, and (6) does not appear to be hydroscopic (we have 1N NMR of tropic acid with no water peak at all). The solvent was a new bottle of dry THF. Therefore, though it is not impossible that some moisture got inside, but certainly there was not a lot of water in the reaction. However, the phenol appears to be the only product formed (and in rather large quantity), besides precursors (5) and tropic acid.

Therefore, the steps suggested by @PatrickThomson are the mostly likely explanation for what is going on. The phenol is most likely formed as tropic acid internally cyclizes, and repels a bare oxygen anion to the triazolopyrazine core, which was then re-protonated in workup. The tropic acid may then undergo a ring opening as I basidified and acidified that reaction in extraction, or maybe not (we do see peaks matching tropic acid in other fractions of the product, but the lactam should have nearly the same 1H peaks as tropic acid).

In this light, the logical thing to do is to follow the protocol of AEW 266-2, AEW 281-1 , and AEW 287-1 to reduce it and attach the THP protection group first, then add it to the ring and deprotect, then oxidize the alcohol to form acidic function group. Since this is the last week of quarter, we have to hand these steps down to the group taking over our project. But we have some (5) to share with them, so there is a good chance of success!

(Just a side note: though our reaction failed, this appears to be a "cool" way to synthesize phenol from halo-aromatics, as it appears to be highly efficient and the conversion rate of (5) to phenol was pretty high throughout. Tropic acid can be recovered after work up, so it worked as a catalyst!)

ghost commented Oct 23, 2016

@PatrickThomson @mattodd Thanks! Internal cyclization could explain why tropic acid is not added to the triazolopyrazine ring, and we are having a "phenol". We generated a 1H NMR spectrum for the phenol:
screen shot 2016-10-23 at 12 21 58 pm

The peak ~ 11.5 ppm appears to match, and the integration of protons is correct! I think this is what we have made. It did not occur to us that 1 H NMR shift of a phenol can be so downfield!

The reaction, as it happened, should be pretty dry. We carefully dried all glassware in oven prior to reaction; precursor (5) was dried in high vacuum overnight, and (6) does not appear to be hydroscopic (we have 1N NMR of tropic acid with no water peak at all). The solvent was a new bottle of dry THF. Therefore, though it is not impossible that some moisture got inside, but certainly there was not a lot of water in the reaction. However, the phenol appears to be the only product formed (and in rather large quantity), besides precursors (5) and tropic acid.

Therefore, the steps suggested by @PatrickThomson are the mostly likely explanation for what is going on. The phenol is most likely formed as tropic acid internally cyclizes, and repels a bare oxygen anion to the triazolopyrazine core, which was then re-protonated in workup. The tropic acid may then undergo a ring opening as I basidified and acidified that reaction in extraction, or maybe not (we do see peaks matching tropic acid in other fractions of the product, but the lactam should have nearly the same 1H peaks as tropic acid).

In this light, the logical thing to do is to follow the protocol of AEW 266-2, AEW 281-1 , and AEW 287-1 to reduce it and attach the THP protection group first, then add it to the ring and deprotect, then oxidize the alcohol to form acidic function group. Since this is the last week of quarter, we have to hand these steps down to the group taking over our project. But we have some (5) to share with them, so there is a good chance of success!

(Just a side note: though our reaction failed, this appears to be a "cool" way to synthesize phenol from halo-aromatics, as it appears to be highly efficient and the conversion rate of (5) to phenol was pretty high throughout. Tropic acid can be recovered after work up, so it worked as a catalyst!)

@KimberleyRoper

This comment has been minimized.

Show comment
Hide comment
@KimberleyRoper

KimberleyRoper Oct 23, 2016

If you think that the acid moiety is the major problem then how about performing the esterification from AEW 266-2 and then trying your SNAr reaction? You could then saponify the ester back to the acid using KOH/Krapcho demethylation conditions if you had the methyl ester. You might have the same problem as above as you've have a similar intermediate (but you could maybe avoid this by decreasing the temperature of saponification?) - overall it would save you quite a few steps and can be run in parallel to your route suggested above.

KimberleyRoper commented Oct 23, 2016

If you think that the acid moiety is the major problem then how about performing the esterification from AEW 266-2 and then trying your SNAr reaction? You could then saponify the ester back to the acid using KOH/Krapcho demethylation conditions if you had the methyl ester. You might have the same problem as above as you've have a similar intermediate (but you could maybe avoid this by decreasing the temperature of saponification?) - overall it would save you quite a few steps and can be run in parallel to your route suggested above.

@ghost

This comment has been minimized.

Show comment
Hide comment
@ghost

ghost Oct 23, 2016

@KimberleyRoper Thanks for the suggestion! Indeed this method did occur to us early on, but we found AEW 267-1, which is exactly the same step---esterification then SNAr. But unlike other reactions of the same type, this one had a really low yield, and we did not see a confirmative NMR of the product attached. At that time, we thought probably tropic acid were forming polymers---stringed together by hydroxyl and carboxylic groups, but with the input from above, it is also possible that an internal cyclization happened with the ester.

ghost commented Oct 23, 2016

@KimberleyRoper Thanks for the suggestion! Indeed this method did occur to us early on, but we found AEW 267-1, which is exactly the same step---esterification then SNAr. But unlike other reactions of the same type, this one had a really low yield, and we did not see a confirmative NMR of the product attached. At that time, we thought probably tropic acid were forming polymers---stringed together by hydroxyl and carboxylic groups, but with the input from above, it is also possible that an internal cyclization happened with the ester.

@mattodd

This comment has been minimized.

Show comment
Hide comment
@mattodd

mattodd Nov 15, 2016

Member

Relevant byproduct being formed:
OC1=CN=CC2=NN=C(C3=CC=C(OC(F)F)C=C3)N21
InChI=1S/C12H8F2N4O2/c13-12(14)20-8-3-1-7(2-4-8)11-17-16-9-5-15-6-10(19)18(9)11/h1-6,12,19H
LKGFFHYSCHTNJQ-UHFFFAOYSA-N
Note added in DCNYS section of wiki. Closing this Issue, though discussion of this byproduct, and hopefully ways to minimise it, should be made in paper. For that, we'll need to make sure the byproduct is properly characterised @RosalindXu

Member

mattodd commented Nov 15, 2016

Relevant byproduct being formed:
OC1=CN=CC2=NN=C(C3=CC=C(OC(F)F)C=C3)N21
InChI=1S/C12H8F2N4O2/c13-12(14)20-8-3-1-7(2-4-8)11-17-16-9-5-15-6-10(19)18(9)11/h1-6,12,19H
LKGFFHYSCHTNJQ-UHFFFAOYSA-N
Note added in DCNYS section of wiki. Closing this Issue, though discussion of this byproduct, and hopefully ways to minimise it, should be made in paper. For that, we'll need to make sure the byproduct is properly characterised @RosalindXu

@mattodd mattodd closed this Nov 15, 2016

@ghost

This comment has been minimized.

Show comment
Hide comment
@ghost

ghost Nov 15, 2016

@mattodd: We have H1 NMR, H1 COSY and C13 NMR on this product.

ghost commented Nov 15, 2016

@mattodd: We have H1 NMR, H1 COSY and C13 NMR on this product.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment