Author Archives: Alexander Kyriacos Tzortzi

Synthesis of (E)-2-chloro-6-(2-(4(pyrrolindin-1-yl)benzylidene)hydrazine)pyrazine from 4-(pyrrolindin-1-yl)benzaldehyde and 2-chloro-6-hydrazinylpyrazine in a condensation reaction #2

AT-1-023 #2

Synthesis of (E)-2-chloro-6-(2-(4(pyrrolindin-1-yl)benzylidene)hydrazine)pyrazine from 4-(pyrrolindin-1-yl)benzaldehyde and 2-chloro-6-hydrazinylpyrazine in a condensation reaction #2

 

Both Reactions were carried out using a microscale to minimalize waste of intermediate product used as reactant.

Reaction 1: Repeat of original condensation reaction

 

 

reaction scheme 

 

 

 

Reagent

Eq

Mw

mmol

w/vol

2-chloro-6-hydrazinylpyrazine

1

144.56

0.2853

41mg

4-(pyrrolindin-1-yl)benzaldehyde

1

175.23

0.2853

50mg

ethanol

~

46.07

~

4ml

 

Experimental Procedure

2-chloro-6-hydrazinylpyrazine (41mg, 0.2853mmol) and 4-(pyrrolindin-1-yl)benzaldehyde (50mg, 0.2853mmol) were added to ethanol (4ml) in a glass vial. The glass vial had a lid put on it and shaken and left to react for 4 hours.

produt.png

TLC analysis (70:30, Pet. Ether/ EtOAc and the final TLC was 1:1 Pet. Ether/ EtOAc) was taken after two hours, showing it hadn’t gone to completion. After 4 hours TLC analysis showed it had.

tlcs.png

In the TLC, on the spots for the product, several isomers had the same r.f. value so it is impossible to tell them apart from TLC. Crude NMR taken and shown to be the same as reaction 2, so the crude products (78.6mg) were combined to column together.

Reaction 2: Acetonitrile and acetic acid

 

 reaction scheme

 

 

Reagent

Eq

Mw

mmol

w/vol

2-chloro-6-hydrazinylpyrazine

1

144.56

0.2853

41mg

4-(pyrrolindin-1-yl)benzaldehyde

1

175.23

0.2853

50mg

Acetonitrile

1

41.05

~

1ml

Glacial acetic acid

~

60.05

~

0.045ml

Experimental Procedure

2-chloro-6-hydrazinylpyrazine (41mg, 0.2853mmol) and 4-(pyrrolindin-1-yl)benzaldehyde (50mg, 0.2853mmol) were added to acetonitrile (1ml) and glacial acetic acid (0.045ml in a glass vial. The glass vial had a lid put on it and shaken and left to react for 4 hours.

produt.png

TLC analysis (70:30, Pet. Ether/ EtOAc and the final TLC was 1:1 Pet. Ether/ EtOAc) was taken after two hours, showing it hadn’t gone to completion. After 4 hours TLC analysis showed it had.

tlcs.png

In the TLC, on the spots for the product, several isomers had the same r.f. value so it is impossible to tell them apart from TLC. Crude NMR taken and shown to be the same as reaction 2, so the crude products (75.5mg) were combined to column together.

Mixed reactions for isomer separation

The acetonitrile (75.5mg) and ethanol (78.6mg) crude products were mixed together (154.1mg). The crude NMR’s had shown the same product produced for both reactions, which contained the correct isomer. The products were dissolved in DCM and TLC systems for the best separation was tested. TLC tank A contained 80:20 Pet. Ether: EtOAc and tank B contained 90:10 Pet. Ether: EtOAc.

Tank C contained 80:20 Pet. Ether: diethyl ether and tank D contained 70:30 Pet. Ether: Diethyl ether.

Finally Tank E contained 70:30 Toluene: acetone.

tlc.png

The best tank for the separation of my crude product was a mixture between tank A and B, with 85:15 Pet. Ether and EtOAc. The crude product was purified via flash chromatography and 50 vials were taken off.

column tlc.png

A single product was present between vials 5-7, 8-12 had a mixture of isomers and 13-48 had a mixture of at least 2 isomers. The pure product betweek vials 5-7 was mostly clean but still contained some water, EtOAc and Pet. Ether. The correct isomer was not isolated however. It was still contained within the mass between vials 13-48.

fractions.png

Due to the very close r.f. values it was very difficult to separate out the isomers (all yellow solids), which meant that this step could not be moved forward because the correct product was not isolated.

 Reference:

  1. Open source malaria: our experiment, http://malaria.ourexperiment.org/triazolopyrazine_se/9268/Synthesis_of_E2chloro62naphthalen2ylmethylenehydrazinylpyrazine_TY_21.html ,date accessed: 04/11/16

 

Cyclisation of (E)-2-chloro-6-(2-(4(pyrrolindin-1-yl)benzylidene)hydrazine)pyrazine (AT-01-23) to form 5-chloro-3-(4-(pyrronlidin-1-yl)phenyl)-[4,3-a]pyrazine (AT-01-25)

AT-1-025

Cyclisation of (E)-2-chloro-6-(2-(4(pyrrolindin-1-yl)benzylidene)hydrazine)pyrazine (AT-01-23) to form 5-chloro-3-(4-(pyrronlidin-1-yl)phenyl)-[4,3-a]pyrazine (AT-01-25) 

reaction scheme 

Reagent

Eq

Mw

mmol

w/vol

AT-01-23

1

300.79

0.7989

0.2403g

DCM

~

84.39

~

15ml

PIDA

1

322.1

0.7989

0.2573g

NaHCO3

~

~

~

30ml

Mg2CO3

~

~

~

~

 

Experimental Procedure

 

(E)-2-chloro-6-(2-(4(pyrrolindin-1-yl)benzylidene)hydrazine)pyrazine (240.3mg, 0.7989mmol) was added to DCM (15ml) in a round bottom flask. PIDA (257.3mg, 0.7989mmol) was also added and the reaction was left to stir at room temperature. On addition to the PIDA, the reaction changed from a bright red solution to a rusty red colour.

IMG_2841.png

The reaction was stirred at room temperature for 7 days, over which time the reaction changed from pale yellow to orange.

IMG_2848 (1).png

Upon completion of the reaction, which was determined by TLC analysis, (5:3 Pet. Ether: Diethyl ether for first TLC, 1:1 hexane: EtOAc for the second TLC plate and 70:30 EtOAc/ Pet. Ether for the third)

IMG_2847.png

The mixture was placed into a separating funnel and the solution was separated into the inorganic and organic layers by the addition of NaHCO3 (30ml). The organic layer was tapped off and the inorganic layer was put to one side. The  organic layer was then washed with DCM (4x30ml). The mixture was then dried by Mg2CO3 and filtered. From the resulting solution a crude NMR was taken.

The solvent from the crude was in vacuo. Silica and EtOAc were added, solvent removed via in vacuo again and then Flash columned, to purify the product.

column.png

Solvent system for the column started at 1:1 Pet. Ether/ EtOAc, but was changed to 70/30 EtOAc/ Pet. Ether to increase the mobile phase. 57 Test tubes were taken. Products appeared in test tubes 3-6, 9-11, 17-20, 21-23, 24, 27-29, 30-33 and 37-57.  

TLC of column.png

The Final product was given as a yellow solid for each of the fractions. None of the products produced were pure, they were all a mix of isomers. No yield was recorded but each fraction from 21-23 onwards had a yield. (0.0202-0.0277g, 9-10%).

 1H NMR showed that the material contained many different isomers of the correct product in the same fractions. Most of them also had water, EtOAc and Pet. Ether impurities.

 

A-1-025.

 

Reference:

  1. Open source malaria: our experiment, http://malaria.ourexperiment.org/triazolopyrazine_se/9259/Synthesis_of_5Chloro124triazolo43apyrazine_TZ_61.html, date accessed: 04/11/16

Synthesis of (E)-2-chloro-6-(2-(4(pyrrolindin-1-yl)benzylidene)hydrazine)pyrazine from 4-(pyrrolindin-1-yl)benzaldehyde and 2-chloro-6-hydrazinylpyrazine in a condensation reaction

AT-1-023

Synthesis of (E)-2-chloro-6-(2-(4(pyrrolindin-1-yl)benzylidene)hydrazine)pyrazine (AT-1-023) from 4-(pyrrolindin-1-yl)benzaldehyde and 2-chloro-6-hydrazinylpyrazine in a condensation reaction

 reaction scheme

 

 

Reagent

Eq

Mw

mmol

w/vol

4-(pyrrolindin-1-yl)benzaldehyde

1

175.23

0.9823

172mg

2-chloro-6-hydrazinylpyrazine

1

144.56

0.9823

142mg

Ethanol

~

46.07

~

8ml

 

Experimental Procedure

 

2-chloro-6-hydrazinylpyrazine (0.142g, 0.9823mmol) and ethanol (8ml) were placed into a round bottom flask. 4-(pyrrolindin-1-yl)benzaldehyde (0.172g, 0.9823mmol) was also added to the round bottom flask. The reaction was stoppered and put on to mix for 2.5 hours.

IMG_2808.png

IMG_2811.png

During this time the colour of the reaction changed from orange to bright red.

TLC’s ( 1:1 pet ether/ EtOAc) had to go through a mini work up before TLC’s could be taken as the mixture was too concentrated and distorted the spots.

IMG_2826.png

The TLC showed the loss of the starting material from the product and the formation of what we assumed to be product. Once this was confirmed, the solvent was removed in vacuo and an NMR was taken. It showed some solvent impurities so the solution was washed in d-chloroform and the solvent was removed in vacuo  again. The Final product was given as an red solid (0.2706g, 0.899mmol, 91%). 1H NMR showed that the product had been formed had some ethanol impurities, even after washing in d-chloroform. Apart from that the product seemed to be clean.

 

crude nmr at-23.png

final nmr at-23.png

at-23 cosy.png

Reference

  1. Open source malaria: our experiment, http://malaria.ourexperiment.org/triazolopyrazine_se/9268/Synthesis_of_E2chloro62naphthalen2ylmethylenehydrazinylpyrazine_TY_21.html, date accessed: 04/11/16

 

Synthesis of 4-(Pyrrolidin-1-yl)benzaldehyde from 4-Fluorobenzaldehyde and Pyrrolidine via SNAr using sonication

AT-1-012

Synthesis of 4-(Pyrrolidin-1-yl)benzaldehyde from 4-Fluorobenzaldehyde and Pyrrolidine via SNAr using sonication

 reaction scheme

 

 

Reagent

Eq

Mw

mmol

w/vol

4-Fluorobenzaldehyde

1

124.11

2.2

0.21ml

Pyrrolidine

3

71.12

2.2

0.18ml

DMSO

-

78.13

-

2ml

K2CO3

1.5

138.21

2.2

0.304g

 

Experimental Procedure

 

Pyrrolidine (0.18ml, 2.2mmol) was added to DMSO (2ml), in a round bottom flask and then anhydrous K2CO3 (0.304g, 2.2mmol) and 4-Fluorobenzaldehyde (0.21ml, 2.2mmol) were added sequentially. The round bottom flask was placed into a sonication machine and turned on and left to react for 15 minutes.

After 15 minutes, a TLC was taken from the mixture (5:3 Pet. Ether: Diethyl ether), this showed the reaction hadn’t moved far due to the large amounts of starting material present in the product. The reaction was put on for a further 45 minutes and a TLC was taken after this time, but it showed almost no change.

IMG_2615.png

The reaction to synthesise 4-(Pyrrolidin-1-yl)benzaldehyde using sonication didn’t produce results, so the previous experiment using SNAr reaction without sonication was decided to be used as the route of synthesis for 4-(Pyrrolidin-1-yl)benzaldehyde as it produced a good yield to move forward. No successfull yield was produced so no NMR data was taken as it was deemed unnecessary.

Reference:

  1. Magdolen, Peter, Tetrahedron, 2001 ,  vol. 57,  # 22  p. 4781 – 4785
  2. Organic-chemistry, sonochemistry, http://www.organic-chemistry.org/topics/sonochemistry.shtm, accessed 16th Oct 2016

 

 

 

 

 

AT-1-012: Synthesis of 4-(Pyrrolidin-1-yl)benzaldehyde from 4-Fluorobenzaldehyde and Pyrrolidine via SNAr

AT-1-012

Synthesis of 4-(Pyrrolidin-1-yl)benzaldehyde from 4-Fluorobenzaldehyde and Pyrrolidine via SNAr

 

 

 

Reagent

Eq

Mw

mmol

w/vol

4-Fluorobenzaldehyde

1

124.11

8

0.9ml

Pyrrolidine

3

71.12

24

1.8ml

DMF

-

73.09

-

15ml

K2CO3

1.5

138.21

12

1.65g

CHCl3

-

119.38

-

5ml

   

 

 

 

 

Experimental Procedure

Pyrrolidine (1.8ml, 24mmol) was added to dry DMF (15ml), in a round bottom flask and then anhydrous K2CO3 (1.65g, 12mmol) were added sequentially. The reaction was stirred for 15 minutes at room temperature. 4-Fluorobenzaldehyde (0.9ml, 8mmol) was then added and the reaction continued to stir and was heated to 80°C. The reaction started off a pale yellow at the beginning of the reaction.

Reaction.png

The reaction was stirred at 80°C for 11 hours, over which time the reaction changed from pale yellow to orange.

Beginning of reaction.png
 
End of reaction.png
 

Upon completion of the reaction, which was determined by TLC analysis, 5:3 Pet. Ether: Diethyl ether. The TLC’s needed a mini work up due to the DMF disrupting the accuracy of the TLC’s.

TLC to show reaction completed.png

The solution was left to cool for 30 minutes, deionised water (30ml) was then added along with DMF (25ml) and then the solution was added to a separating funnel. The solution was then washed with EtOAc 3x, and then the non-organic layer (bottom layer) was taken off.

Before Separation of organic layer.png
 
Separation of organic and inorganic layer.png

The remaining crude product was then washed with brine 3x to remove the DMF. This crude product was then rotor evaporated down. Silica and EtOAc were added, rotor evaporated down and then Flash columned, to purify the product.

Flash column.png

Solvent system for the column started at 80/20 Pet. Ether/ Diethyl ether, but was changed to 70/30 Pet. Ether/ Diethyl ether to increase the mobile phase. 109 Test tubes were taken, with the product being present between 40-100.

Flash column TLC's.png

The Final product was given as an orange solid (1.19g, 6.76 mmol, 84%). 1H NMR showed that the material had petroleum ether impurities, very small amount of starting material and a peak at 3.093ppm which I determined to be Chloromethane. The product was washed again in d-Chloroform 3x and another 1H NMR was taken again and which showed the petroleum ether peaks had decreased, as had the starting material. The peak at 3.093ppm remained however, but this should not affect my next experiment of the condensation reaction to join my product to the pyrazine core.

Product.png

A-1-012.

nmr final.png
 
nmr final 2.png
 
carbon.png
 
carbon2.png
 
image4_.png
 
HMBC.png
 
HSQC.png
 

 

Reference:

1. D. Kumar, K. Raj, M. Bailey, T. Alling, T. Parish and D. Rawat, Bioorganic & Medicinal Chemistry Letters, 2013, 23, 1365-1369.

Synthesis of 4-(Pyrrolidin-1-yl)benzaldehyde from 4-Bromobenzaldehyde and Pyrrolidine via Buchwald-Hartwig Coupling #2

AT-1-012

Synthesis of 4-(Pyrrolidin-1-yl)benzaldehyde from 4-Bromobenzaldehyde and Pyrrolidine via Buchwald-Hartwig Coupling #2

 

 

 

 

Reagent

Eq

Mw

mmol

w/vol

4-Bromobenzaldehyde

1

185.02

2.70

0.50g

Pyrrolidine

1

71.12

2.30

0.19ml

BINAP

0.04

622.67

0.109

0.068g

Na-t-Bu

1.5

96.10

4.06

0.39g

Pd(dba)2

0.03

575.00

0.087

0.05g

Toluene

-

92.14

-

5ml

 

Experimental Procedure

 

4-Bromobenzaldehyde (0.50 g, 2.7 mmol) was added to toluene (5 mL) in a round bottom flask which was then sealed with a septum. Then pyrrolidine (0.19ml, 2.3 mmol), NaO-t-Bu (0.39 g, 4.06 mmol), BINAP (0.068 g, 0.109 mmol) and Pd(dba)2 (0.05 g, 0.087 mmol) were sequentially added to the flask which flushed with N2, and a N2 atmosphere maintained. The mixture was brown/yellow.

 

image1.png
 

 

The reaction was stirred at 70 °C for 2.5 hours, over which time the reaction changed from brown/yellow to green/brown.

 

image2.png

Upon completion, as determined by TLC analysis (85:15 Pet. Ether: Diethyl Ether) the solvent was removed under reduced pressure, EtOAC was added to the oily residue, and the solvent removed again.

 

image6.png
 
image4.png
 
image5.png

 

The crude product was purified by flash chromatography (silica gel; 85:15 Pet. Ether: Diethyl Ether).

image3.png

This produced the product as an orange oil (139mg, 0.195mmol, 29%). 1H NMR showed that the material isolated contained many impurities, which were mainly solvents. The product was washed with chloroform-d and rotor evaporated off, then another NMR sample was taken which proved to be pure apart from what appears to be BINAP between 7.2-8.2ppm. Yield and purity increased but not by enough, SNAr route alternative to be tried.

A-1-012.

crude nmr.png
 
final nmr.png
 
carbon.png
 
carbon2.png
IR_1.png
 
image4_.png
 
HSQC.png
 
HMBC.png

Reference:

1.C. Fattorusso, G. Campiani, G. Kukreja, M. Persico, S. Butini, M. Romano, M. Altarelli, S. Ros, M. Brindisi, L. Savini, E. Novellino, V. Nacci, E. Fattorusso, S. Parapini, N. Basilico, D. Taramelli, V. Yardley, S. Croft, M. Borriello and S. Gemma, J. Med. Chem., 2008, 51, 1333-1343.

Reading University; Synthesis of 4-(Pyrrolidin-1-yl)benzaldehyde from 4-Bromobenzaldehyde and Pyrrolidine via Buchwald-Hartwig Coupling

AT-1-012

Synthesis of 4-(Pyrrolidin-1-yl)benzaldehyde from 4-Bromobenzaldehyde and Pyrrolidine via Buchwald-Hartwig Coupling

 

 

 

Reagent

Eq

Mw

mmol

w/vol

4-Bromobenzaldehyde

1

185.02

1.08

0.20g

Pyrrolidine

1

71.12

1.08

90µL

BINAP

0.04

622.67

0.04

0.027g

Na-t-Bu

1.5

96.10

1.62

0.16g

Pd(dba)2

0.03

575.00

0.03

0.02g

Toluene

-

92.14

-

4ml

 

Experimental Procedure

 

4-Bromobenzaldehyde (0.20 g, 1.08 mmol) was added to toluene (2 mL) in a round bottom flask which was then sealed with a septum. Then pyrrolidine (90 µL, 1.08 mmol), NaOt-Bu (0.16 g, 1.62 mmol), BINAP (0.027 g, 0.04 mmol) and Pd(dba)2 (0.02 g, 0.03 mmol) were sequentially added to the flask which flushed with N2, and a N2 atmosphere maintained. The mixture was brown/yellow.

 

Reaction.png

 

The reaction was stirred at 70 °C for 2.5 hours, over which time the reaction changed from brown/yellow to brown/red.

 

Reaction Colour Change.png

After an additional 30 minutes, further toluene (2 mL) was added. Upon completion, as determined by TLC analysis (60% EtOAc/Pet. Ether) the solvent was removed under reduced pressure, EtOAC was added to the oily residue, and the solvent removed again.

 

TLC.png
 
TLC.1.png

 

The crude product was purified by flash chromatography (silica gel; 85:15 pet. ether: diethyl ether) to furnish the product as an orange oil (33mg, 0.19 mmol, 17%). 1H NMR showed that the material isolated contained many impurities.

 

It was decided to repeat the reaction on larger scale, as it was thought that this would facilitate product isolation. See AT-1-012.

CRUDE NMR.png

3&4 NMR.png

5&6 NMR.png

 

 References:

1. C. Fattorusso, G. Campiani, G. Kukreja, M. Persico, S. Butini, M. Romano, M. Altarelli, S. Ros, M. Brindisi, L. Savini, E. Novellino, V. Nacci, E. Fattorusso, S. Parapini, N. Basilico, D. Taramelli, V. Yardley, S. Croft, M. Borriello and S. Gemma, J. Med. Chem., 2008, 51, 1333-1343.