All Notebooks | Help | Support | About
3rd December 2016 @ 12:13

Date experiment was active 21-29/11/16

TRF25-01 was successfully synthesised via cyclisation of product TRF21-01 (exp 6). However, the yield was low (15%). TRF21-01 exists as two geometric isomers; it was suggested that one isomer (ref 1 shown below) perhaps did not cyclise- accounting for the lack of yield. This was confirmed during exp 6 when TLC27-03 showed the presence of two spots when using TRF21-01 as the SM in the TLC, this also suggested that the two isomers had different rf values and could be isolated through chromatography. For this experiment TRF21-01 was resynthesized using two different solvent systems (reaction A- ethanol, reaction B- acetonitrile/acetic acid) to see if the solvent favoured the formation of one isomer.  

Procedure (Reaction A)

Compound CAS Moles (mmol) Quantity Equiv.

2-chloro-6-hydrazineylpyrazine (TRF17-01)

  0.36 52.3 mg 1.0
Benzaldehyde 100-52-7 0.39 0.04 mL 1.0
Ethanol  64-17-5 68.5 4 mL 190.4


Both reactions were carried out on a micro scale using small glass vials. TRF17-01 (52.3 mg, 0.36 mmol), benzaldehyde (0.04 mL, 0.39 mmol) and ethanol (4 mL) were mixed together. After 2.5 hrs TLC analysis (TLC32-01, Pet. Ether/EtOAc 7:3) confirmed the reaction had reached completion- with no SM present, two dots were present in the product column however, showing the presence of the two isomers. The solvent was removed in vacuo leaving a sand-yellow crude (85.8 mg). 1HNMR data was obtained (NMR32-01-CRUDE; CDCl3), the NMR resembled that of NMR23-01 (NMR taken for TRF21-01 in exp 5) confirming that the same product was made again successfully. 


Procedure (Reaction B)

Compound CAS Moles (mmol) Quantity Equiv.

2-chloro-6-hydrazineylpyrazine (TRF17-01)

  0.37 53.1 mg 1.0
Benzaldehyde 100-52-7 0.39 0.04 mL 1.0
Acetonitrile 75-05-8 19.1 1.0 mL 190.4
Acetic acid (glacial) 64-19-7 0.87 0.05 mL 2.3


TRF17-01 (53.1 mg, 0.37 mmol), benzaldehyde (0.04 mL, 0.39 mmol), acetonitrile (1.0 mL) and glacial acetic acid (0.05 mL) were mixed together. After 2 hrs TLC analysis (TLC36-03, following a mini-work up of the reaction in ethyl acetate and water- Pet. Ether/EtOAc 7:3) confirmed the reaction had gone to completion (similarly two products were shown in the TLC- both isomers). The solvent was removed in vacuo leaving a sand-yellow crude (84.7 mg). 1HNMR data was obtained (NMR37-01-CRUDE; CDCl3). 

The NMR data (HNMR and NOESY) from reactions A and B confirmed the same product was made, it was concluded that the different solvent system did not significantly favour one isomer, so an attempt to separate the isomers by flash chromatography ensued. 

P28-01, picture showing the identical products from reaction A (left) and B (right) in solvent. 


Isomer separation

TRF21-02 and 03 were mixed together; TRF21-04. The solvent was removed in vacuo, new weight obtained was 144.9 mg (note: the combined mass of both reactions products should have equalled 170.05 mg, so there appeared to be a loss of 25.6 mg at some point in the combination). The crude mixture was purified via flash chromatography on silica gel (MP: Pet. Ether/ethyl acetate 9:1). TLC analysis (TLC38-3, Pet. Ether/ethyl acetate 9:1) confirmed 2 products were obtained from the 48 vials. Vials 4-6 produced a bright yellow solid (58.7 mg) and vials 7-39 produced an orange solid (55.7 mg). 

P39-01, picture showing the extracts from the flash purification of TRF21-04, vials 4-6 on the right and vials 7-39 on the left. 

1H NMR data were obtained for vials 4-6 (NMR39-02) and vials 7-39 (NMR39-01). NMR39-01 appeared to show only one product, TRF21-05 (33%). NOESY data was collected, some evidence from the data suggested that the product consisted of a single E-isomer however not enough evidence was available to confirm with confidence. NMR39-02 matched that of NMR39-1 except for some low intensity extra peaks that could not be identified. 


Data and discussion

Vials 7-39, TRF21-05
TLC analysis showed that Vials 7-39 contained one species that fluoresced only when exposed to a long UV wavelength (366 nm). TLC38-02, shows the presence of only one product throughout. TLC's 38-03a and 38-03b shows unknown39-02 fluorescing under 366 nm UV wavelength (left) and not under 254 nm wavelength (right). 

TLC38-02 VIALS 19-30.png

TLC38-02 Pet. Ether/EtOAc 9:1

TLC38-03 (366 nm).png
TLC38-03 (254 nm).png

Pet. Ether/EtOAc 9:1, under UV light (366 nm)                        

Pet. Ether/EtOAc 9:1, under UV light (254 nm)                       

Vials 4-6
Vials 4-6 contained two species (TLC38-01), one of which fluoresced under 366 nm UV light, suggesting a mix of the two unknowns.  

TLC38-01 VIALS 3-6.png

TLC38-01 Pet. Ether/EtOAc 9:1, shaded dots appeared only under a 366 nm UV light 

Product TRF21-05, existed as an orange solid (55.7 mg, 33%) 1H NMR (400 MHz CDCl3) δ 8.6 (1H, s, CHpyraz) 8.2 (1H, s, NH) 8.0 (1H, s, CHpyraz) 7.7 (1H, s, NCH) 7.62 (2H, dd, J 8 Hz, HAr) 7.4-7.3 (3H, m, HArνmax (ATR) /cm-1 3173, 3025, 2961, 2925, 1568 


The two suspected isomers of TRF21-01:



To conclude isomers were not identified, i am not sure if the isomers were able to be separated by flash.
Another idea suggested on the Github (by @tscmacdonald, ref 2) was that a hydrazine-acetone product (shown below) was formed (through impurities) that was mistakenly accounted for as isomers. This product could account for the minor low intensity peaks found in NMR39-01 (vials 4,5,6). Correct identification is proving tricky, theoretically there is no reason as to why isomers about aryl-hydrazine bond should not cyclise as there not many constraining substituents so it makes sense. Perhaps a rerun taking extra care to avoid any acetone impurities would be useful. 



Possible product formed through impurities that has been mistaken for isomers of TRF21-01



Ref 1: Hydrazone switching,, accessed 02/12/
Ref 2: Suggestion by Thomas Macdonald posted on the Gitub,

NOESY data will be uploaded shortly


Attached Files
26th November 2016 @ 23:23

Date experiment was active: 08/11/16

Compound CAS Moles (mmol) Quantity  Equiv.
(E)-2-(2-benzylidenehydrazineyl)-6-chloropyrazine   0.892 0.207 g 1.0
(Diacetoxyiodo)benzene (PIDA) 3240-34-3 0.892 0.28 g 1.0
Dichloromethane 75-09-2 172.3 11 mL 193.1



PIDA (0.2770 g, 0.892 mmol) was added to TRF21-01 (0.207 g, 0.892mmol) in DCM (11 mL), the mixture was stirred for 1.5 hrs. TLC analysis (TLC26-01, Pet. Ether/EtOAc 7:3) shows the presence of a product the SM was still heavily present however, note the SM shows two dots, most likely from TRF21-01’s two geometric isomers. The shaded dots appeared under a longer wavelength (366nm). The reaction continued for 2 hrs, further TLC analysis (TLC27-03; Pet. Ether/EtOAc 1:1, note a more polar system was required and resulted in the SM isomers separating, this will be considered as a starting basis for isomer separation in future synthesis ), showed the presence of 2 products (note this reaction produces iodobenzene as a side product). PIDA (0.03 g, 0.1 equiv.) and DCM (4.5 mL) were added to the mixture and the reaction was left stirring for 18 hrs. A deep orange solution formed (P27-01).

Picture27-01, picture showing the reaction 22 hrs after start time.

TLC analysis (TLC27-04, Pet. Ether/EtOAc 1:1). showed the presence of 3 products. The mixture was diluted with NaHCO3 (15 mL) and washed with DCM (20 mL x 3), the inorganic layer was extracted and then dried over MgSO4 and the solvent was removed in vacuo. A crude product was obtained (83.5 mg). A 1H NMR of the crude was collected (NMR28-01-CRUDE; CDCl3). The crude product was purified via flash chromatography on silica gel (using a range of eluents starting from pet. Ether/EtOAc 7:3 and ascending to pet. Ether/EtOAc 3:7), two products were separated (P28-01)

Picture28-01, picture of two products that were separated via flash column, product corresponding to NMR29-01 is on the left, and product corresponding to NMR29-02 is on the right.  

1H NMR were taken of both products (NMR29-01 + NMR29-02; CDCl3), NMR29-01 appeared to show desired product TRF25-01. The final product existed as a sand yellow solid- TRF25-01 (0.0304 g, 0.13 mmol, 15%).



1H NMR (400 MHz CDCl3) δ 9.35 (1H, s, HCN), 7.87 (1H, s, NCH), 7.59-7.64 (3H, m, CHAr), 7.50-7.55 (2H, m, CHAr)

NMR29-01 (TRF25-01).pdf

Pet. Ether/EtOAc 7:3, permanganate stained

Pet. Ether/EtOAc 1:1, permanganate stained
Pet. Ether/EtOAc 1:1, permanganate stained

Not enough product was formed to obtain Mass spec data. 



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

to InChI=1S/C11H7ClN4/c12-9-6-13-7-10-14-15-11(16(9)10)8-4-2-1-3-5-8/h1-7H  



Open source malaria: our experiment,, date accessed: 04/11/16

Attached Files
26th November 2016 @ 17:23

Date experiment was active: 07/11/16

Compound CAS Moles (mmol) Quantity Equiv.
2-chloro-6-hydrazineylpyrazine 63286-29-3 1.389 0.2095 g 1.0
Benzaldehyde 100-52-7 1.389 0.14 mL 1.0
Ethanol 64-17-5 171.26 10 mL 26.0



TRF17-01 (0.2095 g, 1.389 mmol) was added to ethanol (10 ml) and stirred. Benzaldehyde (0.142 ml) was added, the mixture was stoppered and stirred for 1.5 hrs. TLC  (TLC22-01; Pet. Ether/EtOAc 5:3) shows that the SM had mostly reacted, multiple products were present however. The reaction continued for another 1.5 hrs. TLC (TLC21-03; Pet. Ether/EtOAc 5:3, reaction mixture was separated in ethanol and water) analysis shows the presence of only one product following the mini-workup, reaction had gone to completion, a light orange product had formed (P22-01).

Picture22-01, picture showing the final product before solvent removal. 

The solvent was removed in vacuo to give a light orange solid TRF21-01 (0.207 g, 64%, 0.89 mmol). 1HNMR (NMR23-01; MeOD) was collected. It was deduced from the NMR that the reaction produced two different geometric isomers. Separation of the isomers will be further explored, cylisation will also commence to see how the geometries impact the ring formation. 



Pet. Ether/EtOAc 5:3, permanganate stained

Pet. Ether/EtOAc 5:3, under UV (366nm) 


NMR23-01; MeOD, NMR of crude product (TRF21-01)



ClC1=CN=CC(NN)=N1 to

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



Open source malaria: our experiment,, date accessed: 04/11/16

Attached Files
26th November 2016 @ 14:47

Date experiment was active 24-25/10/16

Synthesis of TRF17-01 (3.8 g, 26.3 mmol, 80%). TRF17-01 will be added to benzaldehyde (other group members will add this product to their respective benzaldehyde complexes) and furthermore will be cyclised to produce the triazolopyrazine core. 



Compound CAS Moles (mmol) Quantity Equiv.
2,6-Dichloropyrazine 4774-14-5 33.55 5.02 g 1.0
Hydrazine hydrate  10217-52-4 33.95 3 mL 1.0
Ethanol  64-17-5 856.3 50 mL 25.0



2,6-dichloropyrazine (5.02 g, 33.55 mmol) was added to ethanol (50 mL) and stirred. Hydrazine hydrate (3.00 mL, 33.95 mmol, 55% in H2O) was added, the mixture was stirred and heated to 80oC. The mixture was a cloudy yellow composition (P17-01).

Picture17-01, picture showing the reaction 30 mins after start time

After 1.5 hrs the mixture became clearer, and the yellow colour persisted. The reaction was heated overnight. After 20 hrs a clear orange solution formed (P17-03), TLC analysis (TLC17-01; pet. Ether/EtOAc 5:3) showed that product had formed and all SM had reacted. 

Picture17-03, picture showing the final product TRF17-01 immediatly after reaction was stopped. 

The solvent was removed in vacuo. The ethanol and unreacted hydrazine hydrate proved to be difficult to remove, the glassware was swapped to a larger RBF to allow the vigorous bumping to persist without product loss, and toluene was added to azeotrope the water. An orange solid formed that was still wet with solvent, some yield was lost due to the toluene melting the weighing boat of which the product was weighed. The product was placed in a vacuum oven at 40 °C for one week to remove the last of the solvent to provide the product as a light brown solid (3.8 g, 26.3 mmol, 80%). An NMR was taken (NMR18-01). Product TRF17-01 was successfully synthesised with no impurities (less yield than predicted however), the solvent proved to be a problem so for future experiments a different solvent system would be recomended.

TRF17-01 will furthermore be used by myself and other group members to produce the triazolopyrazine cores.



NMR18-01 (TRF17-01).pdf

Product TRF17-01 (orange solid, 80%) m.p. 118o1H NMR (400 MHz, CDCl3) δ 8.13 (1H, s, CHAr), 7.90 (1H, s, CHAr), 6.18 (1H, s, CNHNH2), 3.87 (2H, s, NNH2) νmax (ATR) /cm-1 3233, 3078, 1645, 1575, 1433


TLC17-01; pet. Ether/EtOAc 5:3, note the hydrazine must have reacted with the silica plate, however information is still avaiable from the TLC slide. Plate was stained in permanganate solution.


ClC1=CN=CC(Cl)=N1 to ClC1=CN=CC(NN)=N1

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



Open source malaria: our experiment,, date accessed: 22/10/16
For m.p: chemical book,, accessed 06/12/16

Attached Files
21st October 2016 @ 17:16

Date experiment was active: 17-18/10/16

An alternative sonochemical approach to the SNAr reaction was planned to synthesis TRF1-01. The reaction included ultrasonication to agitate the mixtures particles to stimulate the reaction to completion (Ref 2).

Compound CAS Moles (mmol) Quantity Equiv.
Bis(2-methoxyethyl)amine 111-95-5 4.44 0.66 mL 1.0
4-fluorobenzaldehyde 459-57-4 4.44 0.45 mL 1.0
Potassium carbonate 584-08-7 4.44 618 mg 1.0
Dimethyl sulphoxide 67-68-5 56.32 4.0 mL 13.0


Potassium carbonate (818 mg, 4.44 mmol) and bis-(methoxyethyl)amine (0.66 mL, 4.44 mmol) were added to fluorobenzaldehyde (0.45 mL, 4.44 mmol) in DMSO (4 mL). The flask was set up in the sonication apparatus (model: Bronson 2800). Sonication was stopped after 15 minutes, and a cloudy solution had formed (P14-01).

Picture14-01, after 15 minutes in the sonicator a cloudy colourless solution with yellow residue formed 

TLC was taken (TLC14-01; pet. Ether/EtOAc 5:3) but showed SM still present in reaction. The mixture was sonicated again for 30 minutes; the mixture became more yellow in colour (P14-02).

Picture14-02, mixture after 45 minutes in sonicator

A TLC was taken again (TLC14-02; pet. Ether/EtOAc 5:3) and similar to TLC14-01 the SM mixture was present but there appeared to be a more persistent marking in the reaction mixture on the TLC slide. The mixture was placed back into the sonicator for a further 30 minutes, mixtures apperance remained unchanged.
A Third TLC was taken (TLC14-03; pet. Ether/EtOAc 5:3), showed similar results to TLC14-02. As seen in TLC’s 1401-03, the DMSO appeared to be affecting the results and so a mini work up ensued involving water, diethyl ether and the reaction mixture, TLC was taken (TLC15-01; pet. Ether/EtOAc 5:3), the TLC shows more definitive markings than before and that the SM was heavily present but there also appeared to be the presence of some product. The reaction mixture was diluted with water (100 mL), and ethyl acetate (10 mL) was added. The organic phase was separated, and the aqueous phase back-extracted with ethyl acetate 3 times. The combined organic layers were dried over magnesium sulphate, the drying agent was removed by filtration, and the solvent removed in vacuo. Crude 1H NMR data were collected (NMR14-01; CDCl3). 1H NMR appeared to only show the SM p-Fluorobenzaldehyde (TRF-NMR-SM2, data found in exp 2) and the starting amine (bis(2-methoxyethyl)amine).

This was the third unsuccessful attempt of synthesising TRF1-01. Assumptions about the large steric bulkiness and the overall low nucleophilicity of the starting amine could be made to hypothesis why TRF1-01 could not be synthesised. A new plan will be made for synthesis of a different compound.  



TLC-01, TLC of mixture 15 minutes after sonication started, circled spots on TLC showed up under UV (254 nm), plate was stained with potassium permanganate. Spots from right to left are as follows: SM, SM + reaction, reaction


TLC-02, TLC of mixture 45 minutes after sonication started, the plate was stained with potassium permanganate


TLC-03, TLC of mixture 75 minutes after sonication started, the plate was stained with potassium permanganate


TLC-01, TLC of mixture 75 minutes after sonication started (TLC plate shown on the left, write-up from lab book shown on the right). This TLC was taken after performing a mini work up (mixture + ethyl acetate + water) to remove the DMSO that was irritating the previous TLC plates. The plate was stained with potassium permanganate. 


NMR14-1; CDCl3, NMR showing similar peaks to the SM p-Fluorobenzaldehyde  



Magdolen, Peter  
Tetrahedron, 2001 ,  vol. 57,  # 22  p. 4781 – 4785

Ref 2: : Organic-chemistry, sonochemistry,, accessed 16th Oct 2016

Attached Files