Triazolopyrazine Series

The remaining product from BSX 1-1 was used in another reaction of BSX 2-2, producing another batch of 5-chloro-3-(3,5-difluorophenyl)-[1,2,4]triazolo[4,3-a]pyrazine which may be used in later reactions.

Procedure

(E)-2-chloro-6-(2-(3,5-difluorobenzylidene)hydrazinyl)pyrazine (3.56 g, 13.25 mmol) produced in BSX 1-1 was stirred with PhI(OAc)₂ (4.27 g, 1 equivalent) and DCM (126 ml). Reaction left overnight, TLC was taken and indicated completed reaction.

The work up was completed with sodium hydrogen carbonate and DCM before separation using separating funnel. The organic layer this time was the bottom layer due to the density of the DCM.

Organic layer then put under rotary evaporation before purification.

Ethyl acetate (20 ml) was used to dissolve the solid product and then sonicated to introduce all product into solution. The solution was placed on ice to help induce recrystallisation before filtration under high pressure.

The mass of product was 2.16g, 61.2% yield.

HIRAC

Attached below.

Strings

Smiles

ClC1=CN=CC(N/N=C/C2=CC(F)=CC(F)=C2)=N1

to

ClC1=CN=CC2=NN=C(C3=CC(F)=CC(F)=C3)N21

InChi

InChI=1S/C11H7ClF2N4/c12-10-5-15-6-11(17-10)18-16-4-7-1-8(13)3-9(14)2-7/h1-6H,(H,17,18)/b16-4+

to

InChI=1S/C11H5ClF2N4/c12-9-4-15-5-10-16-17-11(18(9)10)6-1-7(13)3-8(14)2-6/h1-5H

The aim of this experiment series is to synthesise a new series 4 analog based on the triazolopyrazine core. More specifically, the attachment of the 3-5-difluorophenyl group on the north-east portion of the molecule. For more information: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/338

Aim of this experiment is to perform nucleophilic aromatic substitution on the upper left hand corner of the triazolopyrazine core produced in BSX 2-1, simiar to the procedure of BSX 3-1 but with 1.00 mmol of core.The Cl atom this time was substituted by a pyridin-2-ylmethanol group.

Procedure

The triazolopyrazine core (267 mg, 1 mmol), pyridin-2-ylmethanol (109 mg, 1 equiv.), KOH powder (196 mg, 3.5 equiv.) and 18-crown-6 (19 mg, 0.07 equiv.) were introduced to a small vial and stirred at room temperature for 20 mins before TLC attached was taken. However, an amount of the reaction mixture was spilled, approximately half, leading to an inaccurate yield for this experiment. TLC was taken with 100% EtOAc solvent mixture. Reaction product was very dark in colour, almost black and quite viscous. 

The reaction mixture was diluted with water before being washed four times with EtOAc, preserving the organic upper layer each time as the aqueous layer was washed. Sufficient brine and MgSO4 were added before the mixture was filtered. The filtrate was transferred to a round bottom flask before being put in the rotary evaporator under low pressure.

Column purification was performed and columns 5-9 and 10-14 yielded evidence of the product and as a result was further tested using NMR. The spectra for NMR are attached below.

NMR spectra reveal possible presence of water in the sample due to a high peak around 1.56.

Overall the spectra showed the successful production of the molecule however there are more peaks than can be expected. I am unsure why.

The yield for this experiment was 17.6%. I believe the low yield was attributed to selecting very few solutions from the column separation. Only 5 tubes were used and the rest discarded were likely to still contain amounts of product.

HIRAC

Attached below.

Strings

SMILES

OCC1=CC=CC=N1

and

ClC1=CN=CC2=NN=C(C3=CC(F)=CC(F)=C3)N21

to

FC1=CC(C2=NN=C3N2C(OCC4=CC=CC=N4)=CN=C3)=CC(F)=C1

InChi

InChI=1S/C6H7NO/c8-5-6-3-1-2-4-7-6/h1-4,8H,5H2

and

InChI=1S/C11H5ClF2N4/c12-9-4-15-5-10-16-17-11(18(9)10)6-1-7(13)3-8(14)2-6/h1-5H

to

InChI=1S/C17H11F2N5O/c18-12-5-11(6-13(19)7-12)17-23-22-15-8-20-9-16(24(15)17)25-10-14-3-1-2-4-21-14/h1-9H,10H2

Aim of this experiment is to perform nucleophilic aromatic substitution on the upper left hand corner of the triazolopyrazine core produced in BSX 2-1. The Cl atom was substituted by a phenylethyl group.

Procedure

The triazolopyrazine core (533 mg, 2.00 mmol), phenylethanol (244 mg, 1 equivalent), KOH (393 mg, 7.00 mmol, 3.5 equiv.) and 18-crown-6 (37 mg, 140.00 micromol, 0.07 equiv.) were stirred with 10 ml toluene at 40C in a small vial. TLC analysis was taken at 30mins showing no presence of starting reagents in the final reaction mixture, suggesting the reaction had completed. Reaction product was quite viscous and dark orange in colour.

The mixture was left to cool to room temperature before 5 ml of water was introduced to dilute the product to transfer into the separating funnel where it was washed three times with 10 ml EtOAc each time. The organic layer was run off and washed with 4 ml water and 3 ml brine. Sufficient Na2SO4 was added to dehydrate the mixture and eventually removed via filtration. The remaining solution was evaporated using a rotary evaporator at low pressure.

The final product was collected and analysed with TLC. This analysis proved difficult as a solvent mixture with appropriate polarity was required. Experimenting with different ratios of dichloromethane, EtOAc and methanol were generally not polar enough to lift the product from the TLC baseline. These plates were recorded in the image TLC1. In the end, 100% EtOAc was used as the solvent and the resulting plate is shown in TLC2 with Rf value approximately 0.45.

An automatic column was then used to purify the product mixture, observing the peak absorbances at individual wavelengths and collecting the filtrate in a rack of test tubes. Initially, the first peak absorbance was collected and analysed using TLC, yielding poor and inconsistent results where some dots failed to rise and others did by different distances. After continuing the column, another absorbance peak was observed and the filtrate was collected into 14 test tubes. TLC analysis results are shown in image CTTLC. The produced plate reflects presence of the desired compound as all dots rose from the baseline to an approximately equal height. Although, the solvent mixture was different to the initial crude product TLC as 1:1 ETOAc and petroleum ether was used. The solutions in the 14 test tubes were then combined and placed into a 500 mL round bottom flask for further rotary evaporation.

Yield for this experiment was 59.9%.

Hazard and Risk Assessment

Attached below.

Strings

SMILES

ClC1=CN=CC2=NN=C(C3=CC(F)=CC(F)=C3)N21

and

OCCC1=CC=CC=C1

to

FC1=CC(F)=CC(C2=NN=C3N2C(OCCC4=CC=CC=C4)=CN=C3)=C1

InChi

InChI=1S/C11H5ClF2N4/c12-9-4-15-5-10-16-17-11(18(9)10)6-1-7(13)3-8(14)2-6/h1-5H

and

InChI=1S/C8H10O/c9-7-6-8-4-2-1-3-5-8/h1-5,9H,6-7H2

to

InChI=1S/C19H14F2N4O/c20-15-8-14(9-16(21)10-15)19-24-23-17-11-22-12-18(25(17)19)26-7-6-13-4-2-1-3-5-13/h1-5,8-12H,6-7H2

The aim of this experiment series is to synthesise a new series 4 analog based on the triazolopyrazine core. More specifically, the attachment of the 3-5-difluorophenyl group on the north-east portion of the molecule. For more information: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/338

The aim of this experiment is to cyclise the ( E)-2-chloro-6-(2-(3,5 difluorobenzylidene)hydrazinyl)pyrazine synthesised in BSX 1-1 to produce the triazolopyrazine core.

Procedure

(E)-2-chloro-6-(2-(3,5-difluorobenzylidene)hydrazinyl)pyrazine (3.68 g, 13.70 mmol) produced in BSX 1-1 was stirred with PhI(OAc)₂ (4.41 g, 1 equivalent) and DCM (126 ml) for approximately 1 hour before TLC analysis was performed revealing no traces of reagents in the "R" reaction mixture lane indicating a completed reaction.

The reaction was quenched by sodium hydrogen carbonate solution (150 ml) and again washed with DCM (50 ml). Combined organic and aqueous layers were then separated. Aqueous layer was preserved.

The organic layer was separated using a separating funnel and dried with sufficient Na2SO4 powder until saturated. The solution was decanted into a round bottom flask and placed in the rotary evaporator for 1 hour at 40C. After this time, a solid substance had settled on the bottom of the flask. The mixture was filtered using a Buchner funnel, leaving a gold crystallised solid in the flask (product BSX2-1a). As the filtrate still contained some product, the solution was again evaporated in the rotary evaporator until dry.

This second evaporation proved difficult as very little solid was produced as the solution was evaporated. Cold petroleum spirits was added to induce crystallisation before the flask was sonicated for 5 minutes. The solution was filtered using the Buchner funnel producing a darker brown solid, more coarse in comparison to the initial evaporation (product BSX2-1b).

Yield was 66.3% 

Hazard and Risk Assessment

Attached below.

Smiles

ClC1=CN=CC(N/N=C/C2=CC(F)=CC(F)=C2)=N1

to

ClC1=CN=CC2=NN=C(C3=CC(F)=CC(F)=C3)N21

InChi

InChI=1S/C11H7ClF2N4/c12-10-5-15-6-11(17-10)18-16-4-7-1-8(13)3-9(14)2-7/h1-6H,(H,17,18)/b16-4+

to

InChI=1S/C11H5ClF2N4/c12-9-4-15-5-10-16-17-11(18(9)10)6-1-7(13)3-8(14)2-6/h1-5H

The aim of this experiment series is to synthesise a new series 4 analog based on the triazolopyrazine core. More specifically, the attachment of the 3-5-difluorophenyl group on the north-east portion of the molecule. For more information: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/338

Condensation of (E)-2-chloro-6-(2-(3,5-difluorobenzylidene)hydrazinyl)pyrazine (BSX 1-1)

This experiment is the first step in the synthesis of a new series 4 analog with a difluorobenzene group in the north east section of the molecule.

The aim of this experiment is to produce (E)-2-chloro-6-(2-(3,5-difluorobenzylidene)hydrazinyl)pyrazine from a condensation reaction involving 2-chloro-6-hydrazinylpyrazine and 3,5-difluorobenzaldehyde. 

Procedure

2-chloro-6-hydrazinylpyrazine (4.00g, 27.67mmol) and 3,5-difluorobenzaldehyde (3.93g, 1 equivalent) were dissolved in ethanol (200ml). This mixture was stirred for 30min at room temperature in a 250ml round bottom flask, yielding an opaque, orange solution. After stirring, TLC analysis was performed using 1:1 hexane and petroleum ether (16ml total solvent). The TLC plate contained three spots, "S" on the left indicating the starting product 2-chloro-6-hydrazinylpyrazine, "R" on the right indicating the solution produced after the reaction was performed and "M" in the middle indicating a mixture of the starting and reaction substances to display all possible spots during TLC analysis. The final plate when placed under UV light revealed no contents of the starting material in the reaction column therefore suggesting a likely completed reaction.

The final reaction mixture was then dried in a rotary evaporator under low pressure before removing and placing into small vials for further analysis and reactions.

Conclusion

This reaction was successfully completed as indicated by TLC analysis. The yield for this experiment was 95.8%.

Hazard and risk assessment

Attached below.

SMILES

ClC1=CN=CC(NN)=N1

and 

FC1=CC(F)=CC(C([H])=O)=C1

to

ClC1=CN=CC(N/N=C/C2=CC(F)=CC(F)=C2)=N1

InChi

InChI=1S/C4H5ClN4/c5-3-1-7-2-4(8-3)9-6/h1-2H,6H2,(H,8,9)

and

InChI=1S/C7H4F2O/c8-6-1-5(4-10)2-7(9)3-6/h1-4H

to

InChI=1S/C11H7ClF2N4/c12-10-5-15-6-11(17-10)18-16-4-7-1-8(13)3-9(14)2-7/h1-6H,(H,17,18)/b16-4+

The aim of this experiment series is to synthesise a new series 4 analog based on the triazolopyrazine core. More specifically, the attachment of the 3-5-difluorophenyl group on the north-east portion of the molecule. For more information: https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/338