Sciencemadness Discussion Board

Synthesis of isotopically labeled octahydrophenazine

BL1996 - 22-8-2019 at 11:04

Hello everyone! I am a biotech student but for some reasons I am doing an internship in a chemical company. As one of my tasks I had to design a synthesis for isotopically labeled octahydrophenazine using relatively cheap labeled precursor, easy procedure without using any “fancy” equipment and of course good yelds. I did some research and I came up with a 5 step route starting with deuterated cyclohexane. I had shown this to my supervisor, he looked at it for like a minute and said – Ok, it is fine. Next day he told me he had ordered 1g of deuterated cyclohexane lol. I came here for some help because I feel like my supervisor doesn’t care about my success or failure in synthesizing this compound and also seems busy and don’t pay much attention when I have some questions. But I care about this little project and want to get it done so here I am =]

The synthesis goes like this

1) Selective chlorination of cyclohexane with cobalt(II) porphiryn complex

Source Khanna, V., Tamilselvan, P., Jeet Singh Kalra, S., & Iqbal, J. (1994). Cobalt(II)-porphyrin catalyzed selective functionalization of alkanes with sulfurylchloride: A remarkable substituent effect. Tetrahedron Letters, 35(32), 5935–5938. https://doi.org/10.1016/S0040-4039(00)78223-2

2) Elimination reaction to get cyclohexene

3) Selective oxidation to cyclohexanone

Source https://www.designer-drug.com/pte/12.162.180.114/dcd/chemist...

4) Bromination with NBS to 2-bromocyclohexanone

As described in this paper Zhang, G., Wang, F., Du, J., Qu, H., Ma, X., Wei, M., & Wang, C. (n.d.). Supporting Information Towards the Total Synthesis of Palhinine A : Expedient Assembly of Multifunctionalized Isotwistane Ring System with Contiguous Quaternary Stereocenters.

5) Condensation with ammonia to octahydrophenazine using microvawe

Utsukihara, T., Nakamura, H., Watanabe, M., & Horiuchi, C. A. (2006). Microwave-assisted synthesis of a -hydroxy ketone and a -diketone and pyrazine derivatives from a -halo and a , a 0 -dibromo ketone, 47, 9359–9364. https://doi.org/10.1016/j.tetlet.2006.10.087

I am testing this procedure using normal unlabeled reagents but unfortunately I accidentally(or maybe by my stupidity) wasted all 20ml of sulfuryl chloride they had. I’ve tried to find a way to synthesize this compound and I found a procedure using gaseous SO2 and Cl2 or by mixing concentrated H2SO4 with PCl5 but I can’t use any of them since they don’t have gaseous SO2 and Cl2 or PCl5. I’ve seen PCl3 on their reagents list but I assume that if I mix it with H2SO4 I won’t get SO2Cl2 as a product but rather something else, right? If reaction with PCl3 doesn’t work is there any other way to make SO2Cl2? If not and they won’t be willing to order some of it how can I get around it? I was thinking about trying a radical bromination but I am not sure if this is a good idea since radical reactions are hard to control. Maybe I can use NBS to selectively brominate cyclohexane in similar way as a cyclohexanone?

My another question is about the elimination reaction. I’ve never done it practically, I only know the mechanism from books. So to perform it I need to dissolve a base(I have KOH, NaOH and t-BuONa) in alcohol(probably methanol), then mix it with halogenated compound. Is it better to add excess of base or equimolar amount? Should I heat it under reflux for some time or should I leave it in room temperature or maybe cool it down?(I think that heating under reflux is the way to go)

In the bromination step they’re using CH2Cl2 as a solvent for NBS, p-TsOH and cyclohexanone but I don’t have any. I have chloroform and I think I can use it instead since it is a similar compound with slightly higher polarity. Am I right?

What do you guys think about this synthesis route? Can I improve it to get the desired product in faster and more efficient way starting with cyclohexane?

PS English isn't my native language so sorry for any grammar mistakes ;p



Metacelsus - 23-8-2019 at 03:02

The later steps (from cyclohexanone) look fine, according to Reaxys. But there may be an easier way to get to the cyclohexanone: direct oxidation by air. See the attached reference. There are various catalysts that can do this.

Attachment: musser2011.pdf (201kB)
This file has been downloaded 1533 times

icelake - 23-8-2019 at 05:05

Cyclohexene can be converted to 2-bromocyclohexanone in one step.

Attachment: bromo ketones from olefins using TsNBr2 (2.4MB)
This file has been downloaded 407 times

Attachment: reaxys 2-bromocyclohexanone.pdf (227kB)
This file has been downloaded 770 times

Edit: New link.

https://www.journal.csj.jp/doi/10.1246/cl.1983.1481

[Edited on 23-8-2019 by icelake]

BL1996 - 23-8-2019 at 10:09

@Metacelsus

I’m afraid that direct oxidation by air won’t work for me because the main problem is that it requires high pressure. I have to ask but I haven’t seen any high pressure reactors there. Another problem is that as the article says

Quote:

cyclohexanol and cyclohexanone, are more readily oxidized than cyclohexane, the conversion of cyclohexane in the air oxidizers must be kept low (usually under 6 %) to maximize yield. Depending on the conversion, the total yield of alcohol, ketone, and hydroperoxide varies from 70 to 90 %.


So to make it work I would have to continuously remove products from the reaction mixture and then separate alcohol from ketone, oxidate the alcohol to ketone and then proceed with next steps. It can be hard to do in a miniscale – I have only 1 gram of deutered cyclohexane which is about 1,3ml to work with.

@icelake
Thanks for bringing up that idea of direct conversion from cyclohexene! Now I have to find a way to synthesize this TsNBr2 from TsOH.


[Edited on 23-8-2019 by BL1996]

[Edited on 23-8-2019 by BL1996]

icelake - 23-8-2019 at 10:34

Can you change the starting material from cyclohexane to cyclohexanol? It would take 2 steps to get to the 2-bromocyclohexanone.

cyclohexanol -> cyclohexene -> 2-bromocyclohexanone

BL1996 - 23-8-2019 at 11:56

Well the D12-Cyclohexane has already been ordered so I must use it as a starting material. From what I found selective and efficient oxidation of cyclohexane either to cyclohexanol or cyclohexanone requires some advanced catalyst that I wouldn't be able to do myself and of course there is no way that they will buy them specially for me.

Metacelsus - 23-8-2019 at 14:08

Ah, you're right about the high pressure (I didn't read closely enough, sorry). But the direct oxidation may be feasible under milder conditions using a catalyst. I'd check Reaxys again just to be sure.

[Edited on 2019-8-23 by Metacelsus]

BL1996 - 28-8-2019 at 08:26

Update
Next week I will get some more sulfuryl chloride and I'll try to make chlorocyclohexane as described in the paper.
I've also tried the bromination procedure with NBS using CHCl3 as a solvent. Strangely when I evaporated the solvent some small crystals appeared together with a liqiud product. I suppose it was because of impurities in NBS but maybe using CHCl3 wasn't as good idea as I thought. Anyway my supervisor managed to get me some of CH2Cl2 and I repeated the reaction using NBS recrystalized from water. I hope that next week I'll be able to do some test to confirm what substances are in fact in the flasks xD
Because there is only about 1 gram of NBS left I'll have to make some more.
I can make photos and provide some sort of reports from my synthesis in this thread If you'd like

icelake - 28-8-2019 at 21:17

Quote: Originally posted by BL1996  
I can make photos and provide some sort of reports from my synthesis in this thread If you'd like


That would be great.

BL1996 - 6-9-2019 at 13:29

I made some N-bromosuccinimide =]
I was following this procedure
http://www.orgsyn.org/demo.aspx?prep=CV2P0562

60g of succinic acid was dissolved in 50ml of water in 500ml RBF and placed in an ice bath. Then about 130ml of 15% aqueous ammonia was added slowly with stirring. After addition of ammonia the solution became cloudy but after about 10minutes of stirring it became clear slighty yellow/brown.

Right after adding ammonia
https://imgur.com/a/8Asx8xL

After ~10minutes
https://imgur.com/a/3SCJwEk

I didn't have a heating mantle with magnecit stirring so I had to improvise. I put an old school heating mantle on a magnetic stirrer and it worked lol. The setup for distillation looked like this
https://imgur.com/a/4lvIJIW

As the recipe says the distillation started at 100C, then the temperature dropped to 97C and the solution became darker. Next the temperature dropped to 90C for few minutes, rised again to 100C for a next few minutes to finally stop at 110C. The solution again got darker. After about 15 the temperature started to rapidly grow to 280C and the solution became black. The product was collected as a yellow, fast solidifying liquid.

The solution at 97
https://imgur.com/a/eJ1dC8s
At 110
https://imgur.com/a/eokM0vR
And over 280
https://imgur.com/a/SoJTkwV

Crude product
https://imgur.com/a/hcT3XqQ

The mass of crude product was 42,00g. I added 42ml of 96% ethanol to the flask and heathed it until all of succinimide dissolved. The solution was allowed to cool in a room temperature and then placed in a freezer for a night.

Succinimide crystals starting to form
https://imgur.com/a/Rnb309J

Pure crystals of succinimide was then filtered under reduced pressure and washed with small amounts of cold 96% ethanol from freezer.

The pure crystals looked like this
https://imgur.com/a/Px9f2nn

Pure crystals had 36,70g which is about 50% of theoretical yield.

Next I put them in a 500ml beaker on an ice bath, dissolved in 50ml of water and added to it a solution of 50ml water, 16h NaOH and 80g of crushed ice. The solution was stirred vigorously with magnetic stirrer. Then a 15ml of bromine was added and stirred for 10minutes after which the product was filtered under reduced pressure and washed with ice cold water untill the filtrate was clear a solution. I wanted to add more bromine, like 20-25ml but unfortunatelly that was all i had. I thought I got more in a flask ;/ The product was a white creamy powder and weighted 44,60g which is 68% of theoretical yield

The NBS
https://imgur.com/a/qOK1l6p

I am thinking about recrystallizing it from hot water because I saw some pictures of it and it looked more like white crystals simmilar to succinimide. I have never used NBS before so I don't know how it should look like.
What do you think?

[Edited on 6-9-2019 by BL1996]

BL1996 - 6-9-2019 at 14:09

I've also tried the chlorination of cyclohexane but it didn't work at all. I didn't get any mono or disubstituted halogenes. After distilling solvents under reduced preassure some brown/green crap was left in a flask that didn't distill even at 100C under reduced pressure(50mbar)

I am thinking that maybe the prophiryn I used wasn't what it should be. My supervisor promised me like 3 weeks ago to make UV-VIS spectra to confirm that I have made this porphiryn cobal complex but of course it was not done. Instead he looked at the product and said "yeah, it looks like it should, use it" After 2 weeks I finally got some more sulfuryl chloride so I used the porphiryn and the reaction failed completly. I followed the protocole described in paper so my only guess is that it wasn't that porphiryn. I'll try to make UV-VIS spectra and analyze it on my own or maybe with your help guys next week. Anyway I used all the porphiryn I had so today I tried to make some more.

I am thinking that maybe the procedure for making it is not right. My supervisor gave me a mini jar that with label "tetrakis(4-methoxyphenyl)porphyrin". It is purple compact pieces but not shiny, I forgot to take picture.
The procedure he gave mi is
Dissolve porphiryn in chloroform
Dissolve cobalt acetate in methanol
Mix it and add some sodium carbonate "as a base to get protons from porphiryn"
Heat under reflux for 2 to 4h

I am not sure if using sodium carbonate is really necessary because
a) it poorly disolves in that solvents
b) i think that it is reacts with cobalt acetate
(CH3COO)2Co+Na2CO3 -> CoCo3 + 2CH3COONa
I checked cobalt carbonate in google images and it looks so simillar to the stuff that stays on the filter after filtration that I am almost sure it does react and really no cobalt gets built into porphiryn and i am using just purified porhpiryn without cobalt inside



icelake - 7-9-2019 at 02:25

The NBS looks a bit yellow, recrystallize it from hot water.

Speaking of metalloporphyrins, there are some Cobalt porphyrin catalysts (among others), which catalyze the oxidation of cyclohexane to cyclohexanone (major product) & cyclohexanol in mild conditions.

Attachment: Metalloporphyrin-Catalyzed Oxidation of Alkanes with Molecular Oxygen in the Presence of Acetaldehyde.pdf (266kB)
This file has been downloaded 363 times

BL1996 - 9-9-2019 at 10:55

I did an UV-VIS spectra of "empty" porphiryn and it seems legit
https://i.imgur.com/P41nzjr.jpg
It has nice peak at about 420nm and 650nm which is consistent with the data on the sigma site
https://www.sigmaaldrich.com/catalog/product/sial/252883
I found a paper about porphyrin synthesis and it seems that Na2CO3 is in fact unnecessary in this reaction.

Quote:

Insertion of metal atoms into prophyrin cavity requires an additionalstep. Generally, metal insertion requires porphyrin to be dissolved in asolvent or mixture of solvents that solubilizes both the poprhyrin andthe metal salt. The problem is that the first one is hydrophobic and thesecond one is hydophilic. Known solvents appropriate for porphyrinmetallation are dimethylformamide (DMF), dimethyl sulfoxide (DMSO),and mixtures or chloroform with methanol.


I didn't have any more of cobalt acetate so today simultaneously with setting 1,2-cyclohexadione dioxime synthesis (which I'll describe in separate theread after finishing it) I tried to make it from cobalt(II) nitrate x 6 hydrate.

Cobalt(II) nitrate was dissolved in small amount of water, then stoichiometric amount of sodium hydroxide was added to obtain cobalt(II) hydroxide. It precipitated initially as a blue than turned into pink which matches google images of it xD

The precipitate was filtered under reduced pressure, transfered to a beaker and acetic acid was added to it. The solution turned intense red and after all of cobalt hydroxide dissolved, acetic acid was evaporated. Small amount of hot water was then added, then colled down and placed in a fridge to recrystallize the product. The initial precipitate looked intense red rather than pink so I am thiniking that I made anhydrous instead of tetrahydrate but we'll see tommorow. If so maybe I'll just add some more water and put it back to frigde to get tetrahydrate crystals.