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Step 4 – SnAr reaction of benzyl alcohol and hydrazine

Reaction scheme snar.jpg

Masses and measurements:

3-(4-bromophenyl)-5-chloro-[1,2,4]triazolo[4,3,a]pyrazine- 0.5627g

3,4-diflurophenylethan-1-ol - 0.370g

NaH - 0.0876g

THF - 15mL


3-(4-bromophenyl)-5-chloro-[1,2,4]triazolo[4,3,a]pyrazine (0.5627g, 1.82mmol) was placed in a RBF and under inert gas, THF (15mL). Still under an inert atmosphere, the 3,4-difluorophenylethan-1-ol (0.370g, 2.34mmol) and the reaction mixture was put under ice, the NaH (0.0876g, 2.19mmol) was added and left to react until TLC analysis confirmed the completion of the reaction. Before the NaH was added the reaction mixture was an orange solution and after addition of the NaH , the reaction mixture turned to a dark brown opaque mixture.

Step 4 reaction mixture.jpg

The reaction was left to react until TLC analysis (1:1 ethyl acetate & petroleum ether) confirmed complete of reaction.

TLC after 3 hours.jpg
TLC after 20 hours.jpg

Once reaction was complete 2M HCl (20mL) was added to quench reaction and the mixture was seperated and extracted using ethyl acetate (3 x 30mL). Upon seperation, the organic layer was orange and the inorganic layer was a pale yellow colour. The organic layers were kept, dried with MgSO4, filtered under vacuo and rotary evaporated to give a dark brown solid crude material (0.95g).

Crude product.jpg

The crude material was run on a flash column (100% ethyl acetate solvent) and TLC analysis confirmed that test tubes 13-30 contained the final product. Test tubes 13-30 were collected in a RBF and rotary evaporated to give a dark green/brown solid (0.1318g, 16.79%).

Start of flash column.jpg
Progress of flash column.jpg
End of flash column.jpg



Step 3 – synthesis of 3,4-difluorophenylethan-1-ol

Step 3.jpg

Masses and measurements:

3,4-difluorophenyl acetic acid - 0.9934g

LiAlH4 - 0.2386g

THF - 6.3mL


The 3,4-difluorophenyl acetic acid (0.9934g, 5.78mmol) was added to a RBF and was dissolved in THF (6.3mL). The reaction mixture was further stirred whilst the LiAlH4 (0.2386g, 6.29mmol) was added and the reaction mixture was stirred under reflux for 2-3 hours or until TLC analysis (1:1 ethyl acetate & petroleum ether) confirmed the completion of the reaction. Around 20mins after all reagents were added, the mixture turned a deep red and soon after turned to a pale yellow solution.

reaction of alcohol.jpg
alcohol synthesis.jpg

Once the reaction was complete, the reaction mixture was left to cooland quenched with 25% NaOH (10mL) and the product was seperated and extracted using 2M HCl (20mL) and ethyl acetate (20mL). Seperation of the reaction mixture gave 2 colourless solution layers. The aqueous layers were re-extracted using diethyl ether (20mL) - it was learnt in the research we underook that the alcohol product is very volatile so diethyl ether was used as it has a lower volatilty to match that of the final product. The organic layers were collected, dried using MgSO4 and filtered under vacuo. The filtrate was rotary evporated with a small amount of solvent present still. The product given was a pale yellow oily solution (0.729g, 79.85%).

Synthesis of 5-(3,4-difluorophenethoxy)-3-(4-(pipperidin-1-yl)phenyl)-[1,2,4]triazolo[4,3-a]pyrazine


VTM010 (0.05 g, 0.12 mmol) was dissolved in degassed toluene (2 mL). Piperidine (0.025 g, 0.29 mmol), NaOtBu (0.016 g, 0.168 mmol), JohnPhos (1.6 mg, 5.4 μmol) and Pd 2 (dba) 2 (0.3 mg, 0.6 μmol) were added to the solution and stirred at 100°C for two weeks. The reaction was quenched with 2M HCl and the organic layer extracted (EtOAc 3x2 mL). The crude was concentrated under reduced pressure and purified via column chromatography (100% EtOAc).

VTM012 COLUMN.jpeg

Synthesis of 5-(3,4-difluorophenethoxy)-3-(4-(pyrrolidin-1-yl)phenyl)-[1,2,4]triazolo[4,3-a]pyrazine


VTM010 (0.05 g, 0.12 mmol) was dissolved in degassed toluene (2 mL). Pyrrolidine (0.02 g, 0.288 mmol), NaO t Bu (0.016 g, 0.168 mmol), JohnPhos (1.6 mg, 5.4 μmol) and Pd 2 (dba) 2 (0.3 mg, 0.6 μmol) were mixed in this order and stirred for two weeks at 100°C. The reaction was quenched (2M HCl). The organic layer was extracted (3x2mL EtOAc). The crude was concentrated in vacuo and purified via column chromatography (EtOAc).


NMR analysis suggested that a final product was not formed.

Synthesis of 3-(4-bromophenyl)-5-(3,4-difluorophenethyl) – [1,2,3]triazolo[4,3-a]pyrazine



VTM009 (0.738 g, 1.22 mmol) was added to a solution of 3,4-difluorophenyl-1-ol (0.60 g, 4.16 mmol) in dry THF (30 mL). The mixture was cooled down to 0°C and NaH (60%, 0.17 g, 6.93 mmol)was added. The mixture was stirred at room temperature for 2 hours. The reaction was quenched with HCl (30mL) and the organic layer extracted with EtOAc (3x30 mL) and 2M HCl (3x10 mL). The crude was concentrated under reduced pressure

VTM010 CRUDE (2).jpg

and purified via column chromatography (100% EtOAc) to yield the final product (0.50 g, 95%) as a beige solid.

VTM010 PRODUCT (3).jpg

Attempted synthesis of final product using Buchwald-Hartwig cross-coupling on a larger scale


Synthesis of final product using Buchwald-Hartwig cross-coupling - on a larger scale



mechanism final step.jpg
Compound Data(mr/density) 


 mMol Eqv 
NH1-007 412.9  0.100g  0.24 
Toluene 4.00ml  -
Pyrrollidine  71.2/0.85g/ml  0.048ml 0.28 1.2 
NaOtBu 96.1  0.0323g  0.34  1.4 
Pd(dBA)2  575.00 0.00069g  0.0012  0.50% 
Johns Phos 298.40 0.00322g 0.0108 4.5%

Procedure- NH1-008

NH1-007 (0.100g, 0.24mmol) was dissolved in degassed toluene (4.00mL). Pyrrolidine (0.048mL,0.28mmol) was added dropwise. John Phos (0.00322g, 0.0108mmol) was added followed by the base, NaOtBu (0.0323g, 0.34mmol). Pd(dBA)2 (0.00069g, 0.0012mmol) was added and the reaction was left to stir at 80 degrees for 7 days.

NH1-008 was separated using HCl and EtOAc. This was then dried using MgSO4, filtered and dried in vacuo. TLC was carried out (5% MeOH/95% DCM) and is shown below.

final TLC.jpg

1H NMR of NH1-008 was taken in chloroform. The NMR did not show the significant product peaks. To confirm this, NH1-008 was purified via flash column chromatography (2% MeOH/98% DCM). The TLC concluded a potential product in vials from 9-16. These were collected and dried in vacuo. 1HNMR was taken but unfortunately the analysis concluded that this reaction did not work as the spectra was same as the starting material.

Repeated SnAr Reaction


SNAr reaction 


week 3.jpg

Reagent Equivalent Molecular Weight mMol Quantity
4-flurophenylethan-1-ol 2 140.00 7.10 0.9mL
Sodium Hydride 2 24.00 14.06 540.00mg
Triazolopyrazine 1 309.55 3.55 1100.00mg
THF - - - 30.00mL


THF (30.00mL) was added to Triazolopyrazine (1100.00mg, 3.5mmol) and the mixture was stirred under a nitrogen atmosphere. 4-flurophenylethan-1-ol (0.9mL, 7.10mmol) was added and the mixture was cooled in ice. NaH (540.00mg, 14.06mmol) was added and the dark brown mixture was stirred and left under a nitrogen atmosphere for 2 hours (RMTP).  

nitrogen atmosphere.jpg

TLC analysis (Petroleum ether/EtOAc 25:75) confirmed that the reaction had worked.

HCl (2M) and EtOAc (60.00mL) were added to separate the solution, the sample was filtered. The solution was dried over MgSO4 which was filtered off and rinsed with EtOAc. The solution was evaporated in vacuo. 

The crude was purified via flash column chromatography (100% Ethyl acetate). TLC analysis (100% ethyl acetate) showed that test tubes 19-57 contained the product.

repeat 1-15.jpg
repeat 17-32.jpg
repeat 33-47.jpg
repeat final 57.jpg

The product was collected and dried in vacuo. This formed golden crystals.

1H NMR of the product NH-1-007 was taken in chloroform. The NMR showed the desired structure.

The product was weighed and dissolved in CDCl3 to ensure that no product was left in the round bottom flask. This was left to dry. The product was re-weighed (360.00mg, 0.87mol, 24%)

Analysis of product NH-1-004

δH(400 MHz, CDCl3: 9.01 (3H, s, CHAr), 7.61 (4H, d, CHAr), 6.91 (2H, d, CHAr), 6.78 (2H, d, CHAr) 4.42 (6H, s, CHAr) and 2.94 (6H, s, CHAr).


Further Analysis of NH1-005-3

NH1-005-3= NH1-006

Further Analysis of NH1-006


mechanism final step.jpg



TLC was carried out in three different solvents which is shown below. The first plate was carried out in 100% EtOAc, the second plate was carried out in 5% MeOH/ 95% DCM and the third plate was carried out in 50% EtOAC/ 50% Pet.Ether.

TLC 3 different solvents.jpg

NH1-006 was purified via flash column chromatography (2% MeOH/ 98% DCM) on a small scale.

small scale FCC.jpg

The TLC concluded a potential product in vials 3-6.  These vials were collected and dried in vacuo.

TLC NH-006 fluoro.jpg

1H NMR and 19F NMR of the product NH-1-006 was taken in chloroform.

Analysis of product NH-1-006

δH(400 MHz, CDCl3: 9.95 (1H, s, CHAr), 7.52 (4H, d, CHAr), 6.80 (5H, q, CHAr), 6.60 (5H, q, CHAr) 4.37 (2H, d, CHAr), 3.36 (4H, s, CHAr), 2.97 (2H, d, CHAr) and 2.05 (5H, s, CHAr).

δF(370Mhz), CDCl3: -115.4 (1F)

The reaction showed a potential product. However, as this reaction was carried out using such a small scale it is difficult to confirm that the reaction had worked to completion. Therefore this reaction needs to be repeated on a larger scale.

Biological Data from Dundee – Oct 2017 Compounds

A set of 26 Series 4 Triazolopyrazine compounds were sent to have their efficacy evaluated against Plasmodium flaciparum in-vitro at Dundee (GitHub issue #8)

The data has been posted here


MMV1576784 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCC/C4=C/BBBBBBBBBB4)N32 InChI=1S/C16H22B10F2N4O2/c27-16(28)34-12-3-1-10(2-4-12)15-31-30-13-8-29-9-14(32(13)15)33-6-5-11-7-17-19-21-23-25-26-24-22-20-18-11/h1-4,7-9,16-26H,5-6H2/b11-7- AGPVLTOPROUGPQ-XFFZJAGNSA-N
MMV1576785 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCC(N4CCOCC4)C5=CC=CC=C5)N32 InChI=1S/C24H23F2N5O3/c25-24(26)34-19-8-6-18(7-9-19)23-29-28-21-14-27-15-22(31(21)23)33-16-20(17-4-2-1-3-5-17)30-10-12-32-13-11-30/h1-9,14-15,20,24H,10-13,16H2 NLNZVWQRJHUCOA-UHFFFAOYSA-N
MMV1576786 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCCN4CC5(COC5)C4)N32 InChI=1S/C19H19F2N5O3/c20-18(21)29-14-3-1-13(2-4-14)17-24-23-15-7-22-8-16(26(15)17)28-6-5-25-9-19(10-25)11-27-12-19/h1-4,7-8,18H,5-6,9-12H2 CWOUGAWUCYKRFC-UHFFFAOYSA-N
MMV1576787 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCC4=CC=C(CO)C=C4)N32 InChI=1S/C20H16F2N4O3/c21-20(22)29-16-7-5-15(6-8-16)19-25-24-17-9-23-10-18(26(17)19)28-12-14-3-1-13(11-27)2-4-14/h1-10,20,27H,11-12H2 VIQWBWLDUDXSBJ-UHFFFAOYSA-N
MMV1576788 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCCC4COC4)N32 InChI=1S/C17H16F2N4O3/c18-17(19)26-13-3-1-12(2-4-13)16-22-21-14-7-20-8-15(23(14)16)25-6-5-11-9-24-10-11/h1-4,7-8,11,17H,5-6,9-10H2 VMXSRABLXQMXLK-UHFFFAOYSA-N
MMV1576789 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCC4(OCCO4)C5=CC(F)=C(F)C=C5)N32 InChI=1S/C22H16F4N4O4/c23-16-6-3-14(9-17(16)24)22(32-7-8-33-22)12-31-19-11-27-10-18-28-29-20(30(18)19)13-1-4-15(5-2-13)34-21(25)26/h1-6,9-11,21H,7-8,12H2 UAZNIGDYRZOARG-UHFFFAOYSA-N
MMV1576790 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCC/C4=C/BBBBB[BH]5[BH]([H]5)BB4)N32.[Cs+] InChI=1S/C16H22B9F2N4O2.Cs/c26-16(27)33-12-3-1-10(2-4-12)15-30-29-13-8-28-9-14(31(13)15)32-6-5-11-7-17-19-20-21-23-25-24(34-25)22-18-11;/h1-4,7-9,16-25H,5-6H2;/q;+1/b11-7-; GZUNPULXOLJYSG-AJULUCINSA-N
MMV1576791 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCC(N(CC)CC)C4=CC(F)=C(F)C=C4)N32 InChI=1S/C24H23F4N5O2/c1-3-32(4-2)20(16-7-10-18(25)19(26)11-16)14-34-22-13-29-12-21-30-31-23(33(21)22)15-5-8-17(9-6-15)35-24(27)28/h5-13,20,24H,3-4,14H2,1-2H3 FFKUJTSUMDVIQH-UHFFFAOYSA-N
MMV1576792 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OCC(N(CC)C)C4=CC(F)=C(F)C=C4)N32 InChI=1S/C23H21F4N5O2/c1-3-31(2)19(15-6-9-17(24)18(25)10-15)13-33-21-12-28-11-20-29-30-22(32(20)21)14-4-7-16(8-5-14)34-23(26)27/h4-12,19,23H,3,13H2,1-2H3 XPBTWBXREHLVRP-UHFFFAOYSA-N
MMV1576793 FC1=CC(CCOC2=CN=CC3=NN=C(C4=CC=C(C(N)=O)C=C4)N32)=CC=C1F InChI=1S/C20H15F2N5O2/c21-15-6-1-12(9-16(15)22)7-8-29-18-11-24-10-17-25-26-20(27(17)18)14-4-2-13(3-5-14)19(23)28/h1-6,9-11H,7-8H2,(H2,23,28) INLVQLIAJLYDGP-UHFFFAOYSA-N
MMV1576794 FC1=CC(CCOC2=CN=CC3=NN=C(C4=CC(C(N)=O)=CC=C4)N32)=CC=C1F InChI=1S/C20H15F2N5O2/c21-15-5-4-12(8-16(15)22)6-7-29-18-11-24-10-17-25-26-20(27(17)18)14-3-1-2-13(9-14)19(23)28/h1-5,8-11H,6-7H2,(H2,23,28) SUVZMBHYRLCWQO-UHFFFAOYSA-N
MMV1576795 FC1=CC(CCOC2=CN=CC3=NN=C(C4=CC=C(C(N(C)C)=O)C=C4)N32)=CC=C1F InChI=1S/C22H19F2N5O2/c1-28(2)22(30)16-6-4-15(5-7-16)21-27-26-19-12-25-13-20(29(19)21)31-10-9-14-3-8-17(23)18(24)11-14/h3-8,11-13H,9-10H2,1-2H3 VILLYIKHHVUPAT-UHFFFAOYSA-N
MMV1576796 BrC1=NN=C2C=NC=C(OCCC3=CC(F)=C(F)C=C3)N21 InChI=1S/C13H9BrF2N4O/c14-13-19-18-11-6-17-7-12(20(11)13)21-4-3-8-1-2-9(15)10(16)5-8/h1-2,5-7H,3-4H2 MNOZFILPXCZGRJ-UHFFFAOYSA-N