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23rd September 2016 @ 17:25

 20 September 2016

Synthesis of EVKCN_Prod3.png

Reference

Holsinger, L.J., Compounds that Inhibit Protease Cathepsins and HCV Replication. U.S. Patent 2008080785, April 30, 2009. 


Data Table
Substance Quant. Mol. wt. mmoles Equiv.
methyl 6-chloropyrazine-2-carboxylate 0.58 g 172.57 3.36 1
dimethoxy ethane 10 mL 90.12     
trimethylsilyltrifluoro-methane 0.70 g  142.2 4.92 1.5 
caesium fluoride 0.051 151.9 3.36  1
THF 4.0 mL 72.11     
acetic acid 2.0 mL 60.05     
tertbutylammoniun fluoride 0.90 g 261.46   3.4 1
ethyl acetate 50 mL 88.11     
1-(6-chloropyrazin-2-yl)-2,2,2-trifluoroethan-1-one

0.71 g (theoretical)

0.07 g (actual)

209.98

3.36 (theoretical)

0.33 (actual)

1 (theoretical)

0.1 (actual)


Procedure
  1. Dissolved starting material in dimethoxy ethane (10 mL). 
  2. Added trimethylsilyltrifluoro-methane (0.70 mL) and caesium fluoride (0.051 g). 
  3. Stirred at room temperature overnight. Solution turned a dark yellow, then brown color. 
  4. Concentrated mixture under reduced pressure, resulting in a dark brown oil. 
    Step 3 brown oil.jpg
     
  5. Dissolved resulting residue in THF (4.0 mL) and acetic acid (2.0 mL) 
  6. Added tertbutylammonium fluoride (0.867 g) 
  7. Allowed reaction to stir overnight. 
  8. Diluted reaction with ethyl acetate (50 mL) 
  9. Washed three times with dilute aqueous sodium bicarbonate solution (0.25M, 100 mL portions). 
  10. Washed with brine (100 mL) 
  11. Dried over anhydrous magnesium sulfate, then filtered. 
  12. Removed solvent under reduced pressure. 
  13. Triturated with a 1:1 dichloromethane/hexanes solution (50 mL), causing a dark brown semi-solid to precipitate from solution. Results were not consistent with literature precedent.  
  14. Removed solvent under reduced pressure, concentrating product back into a dark brown oil. 
    Dark brown oil re-rotovap.jpg
  15. Crude product (dark brown oil) was tested via TLC.
    Left = SM, Center = cospot, Right = product
    TLC Crude Product 3.jpg

    1:1 EtOAc:Hexanes solvent system; silica gel plate; UV visualization
    Rf(bottom) = 0.25, Rf(middle) = 0.42, Rf(top) = 0.50
  16. Purified solution using Biotage Isolera. Fractions 2, 3, 6 and 7 were shown to most likely contain the purified product.
    Step 3 Biotage Screen.JPG
  17. Fractions were analyzed using TLC, GCMS, and NMR. Analysis of the results showed that fractions 6 and 7 contained the most pure sample of product 3, 1-(6-chloropyrazin-2-yl)-2,2,2-trifluoroethan-1-one.
  18. Fractions 6 and 7 were combined and solvents removed in vacuo in preparation for step 4. 
Observations and Analysis

TLC: 
From bottom to top: Fraction 2, 3, 6, 7
TLC Product 3 Fractions.jpg
1:1 EtOAc:Hexanes solvent system; silica gel plate; UV visualization
Rf(2, 3) = 0.50, Rf(6, 7) = 0.24
Fraction 2 potentially contained an impurity in addition to the less polar compound in Fraction 3. 
Fraction 3 contained one less polar compound.
Fractions 6 and 7 contained a second more polar compound.
The fractions were further analyzed by GCMS to determine which was our compound of interest. 
 
GCMS:
Fraction 2 - visualized 2 distinct retention times, indicative of an impurity
EVKCN_Step3_Frac2_GCMS-1.jpg
EVKCN_Step3_Frac2_GCMS-2.jpg
 
 
Fraction 3 
EVKCN_Step3_Frac3_GCMS-1.jpg
EVKCN_Step3_Frac3_GCMS-2.jpg
 
 
Fractions 6 and 7 (combined)
EVKCN_Step3_Frac6_GCMS-1.jpg
EVKCN_Step3_Frac6_GCMS-2.jpg

NMR: 1H-NMR (DMSO, 500MHz), 13C-NMR (DMSO, 126 MHz) measured in ppm
1H and 13C-NMR for starting material, methyl 6-chloropyrazine-2-carboxylate, can be found in Synthesis of methyl 6-chloropyrazine-2-carboxylate (EVKCN 1-2).

1H-NMR for product, 1-(6-chloropyrazin-2-yl)-2,2,2-trifluoroethan-1-one
Wideview
EVKCN_Prod3_1HNMR_Wide_Revised.jpeg
 
Closeup 
EVKCN_Prod3_1HNMR_Close_Revised.jpeg
∂ 8.90 (s, 1H), 8.88 (s, 1H)
 
13C-NMR for product, 1-(6-chloropyrazin-2-yl)-2,2,2-trifluoroethan-1-one.
Wideview
EVKCN_Prod3_13CNMR_Wide_Revised.jpeg
Closeup
EVKCN_Prod3_13CNMR_Close_Revised.jpeg
∂ 152.56, 150.13, 147.54, 145.54, 142.29, 124.45 

Conclusions and Next Steps 

     From our TLC, GCMS, and NMR data, we have concluded that we produced some of our desired product, 1-(6-chloropyrazin-2-yl)-2,2,2-trifluoroethan-1-one. TLC of the crude product indicated an incomplete reaction as some UV-visualizable spots characteristic of the starting material were present in the product. However, after submitting the crude product to the Biotage Isolera, it appeared that we acheived some separation upon TLC and GCMS analysis. Although Fraction 2 appeared to contain some impurity in the TLC, fractions 3, 6, and 7 appeared to be fairly pure (with 6 and 7 containing the same product). We combined fractions 6 and 7, then submitted the 3 samples to GCMS. We found the combined fractions 6 and 7 appeared to be out desired product as we observed the M+ of m/z 209.98, which is characteristic of 1-(6-chloropyrazin-2-yl)-2,2,2-trifluoroethan-1-one. However, upon analysis by NMR, we found that our product also likely contained the more reduced version of the product, 2-(6-chloropyrazin-2-yl)-1,1,1,3,3,3-hexafluoropropan-2-ol. This is evidenced by by the m/z 279.9, 281.9 in GCMS, as well as the peaks at 8.07 and 5.73 ppm in the 1HNMR. 

2-(6-chloropyrazin-2-yl)-1,1,1,3,3,3-hexafluoropropan-2-ol. .png

2-(6-chloropyrazin-2-yl)-1,1,1,3,3,3-hexafluoropropan-2-ol (Image courtesy of Chase Smith via Github)

In any repeat trials, shortening the reaction, running it at 0 deg. C, and/or reducing the amount of trimethylsilyltrifluoro-methane to 1 equivalent, may help to increase the yield of our desired product (advice courtesy of Chase Smith via Github).

     Because we produced primarily the desired product, we continued on with step 4 in which we will perform a reductive amination in an attempt to produce N-benzyl-1-(6-chloropyrazin-2-yl)-2,2,2-trifluoroethan-1-amine. However, for future trials, it may be more effective to perform another separation using Biotage Isolera in order to achieve a more pure product.  

 

Linked Entries
Attached Files
Dark brown oil re-rotovap.jpg
TLC Crude Product 3.jpg
Step 3 brown oil.jpg
TLC Product 3 Fractions.jpg
Step 3 Biotage Screen.JPG
EVKCN_Step3_Frac2_GCMS-1.jpg
EVKCN_Step3_Frac3_GCMS-1.jpg
EVKCN_Step3_Frac2_GCMS-2.jpg
EVKCN_Step3_Frac3_GCMS-2.jpg
EVKCN_Step3_Frac6_GCMS-1.jpg
EVKCN_Step3_Frac6_GCMS-2.jpg
EVKCN_Prod3_1HNMR_Wide_Revised.jpeg
EVKCN_Prod3_1HNMR_Close_Revised.jpeg
EVKCN_Prod3_13CNMR_Close_Revised.jpeg
EVKCN_Prod3_13CNMR_Wide_Revised.jpeg