MJE4- Benzimidazole Synthesis Step 1

[memm0740]

HIRAC- H-MJE4-1.docx

Reaction Scheme

[memm0740]

NMR of starting reagents: S5- NMR starting reagents.pdf

[memm0740]

Method

04/04/23 11:50am

1. Added benzenediamine (0.299g, 1.60mmolr), 1,2-dimethoxyethane (5mL) and methanol (1mL) to make slurry.
2. Then added thiourea (0.602g, 2.92mmol).
3. Reflux started at 11:50am on 04/04/23 till 3:50pm on 06/04/23 (1d, 16hrs or total 40hrs).

04/04/23 4:45pm

• TLC in 9:90:1 MeOH:DCM:NH3

Details - streaking, strange 2 spots for SM only spotted benzenediamine, possibly decomposition. Ammonium hydroxide should stop streaking.

06/04/23 9:02am

• TLC in same solution.

Details- no improvement, can't discern product

06/04/23 2:15pm

• TLC in same solution.

Details- product less sticking to silica, near solvent front.

06/04/23 2:15pm

• NMR crude product

MJE4-1 crude.pdf

• Mass spec

MJE4-1 crude ms.pdf Details- only negative ions detected.

06/04/23 3:50pm

• TLC in 5% MeOH

Details - highly likely product at the top of plate, less polar eluent to see product.

06/04/23 4:30pm

5. Work up reaction
   • dilute reaction mixture with 25mL diethyl ether, then rotor vap

11/04/23 10:00am

• continue working up reaction- rinse with diethyl ether (7mL x 3)
• decant by pipetting out ether after each round

• collect into vial and rotor vap off ether vial= 15.9233g vial + crude product= 16. 3032g

  • NMR crude 2

MJE4-1cr.2.pdf Details- too much solvent

12/04/23 9:30am

• left on house vacuum overnight

• NMR after vacuum and NMR of ether rinses

MJE4-1.r.pdf Details- peaks overshadowed by thiourea peaks, no aromatic peaks

• combined rinses to final product and rotor vap (11:50am- 12:15pm)

• new weight (with rinses)- 16.5330g

• purify by running column- TLC to determine best composition

1. 12:26pm TLC 10% MeOH/DCM Rf= 3.3/3.6= 0.916 (too high)

2. TLC 5% MeOH/DCM Rf= around 1

3. TLC 2% MeOH/DCM Rf= 3.3/3.8= 0.8684

4. TLC 10% EtOAc/Hex Rf= 1.8/3.6=0.5

5. TLC 5% EtOAc/Hex Rf= 1.2/4.1= 0.29268

   • 3:15pm silica column in 5% EtOAc/Hex
   • 3:50pm combine fractions 1-7 and rotor vap
   • NMR

MJE4-1col.pdf Details- possibly thiourea (SM) or derivative

• 4:45pm transfer to vial and rotor vap vial= 15.77g vial + product= 15.906g

13/04/23 1:30pm

• TLC of reaction mixture against thiourea

1. 2% MeOH/DCM
2. 9% MeOH/DCM
3. 5% EtOAc/Hex (less polar, less travelling)

17/04/23 2:30pm

• 2:30pm Mass spec of final compound MS final.pdf Details-

[memm0740]

MJE4-2 Method

17/04/23 9:30am

1. Added benzenediamine (0.293g, 1.58mmol), 1,2-dimethoxyethane (5mL) and methanol (1mL) to make slurry (stirred for 10min). Solvents dried over 3 days.
2. Then added thiourea (0.614g, 3.00mmol). Started reaction at 10:15am. Set temperature at 120C. Reflux started at 10:24am, temp-107C. Reaction continued temp-115C 17/04/23 till 9am on 19/04/23 (1d, 22hrs 36 minutes or total 46hrs)

17/04/23 2:20pm

• TLC 5% ETOAc/Hex

18/04/23 9:23am

• TLC in 5% EtOAc/Hex

  Details- check against both thiourea and diamine (SM), no discernable spots for RM

18/04/23 4:05pm

• TLC in 5% EtOAc/Hex

  

• NMR in CDCl3

19/04/23 9am

• stopped reflux
• TLC 5% EtOAc/Hex, against both SM
• RM volume looks very reduced - dark brown solid (wet)

20/04/23 9am

• Mass spec at end of reflux MJE4-2 after reflux.pdf

24/04/23 10:40am

3. Work up
   • add 10ml diethyl ether total to rinse (x2)
   • add 20 mL DCM to dissolve RM to transfer to vial and rotor vap
   • NMR to check wetness MJE4-2.rv.pdf

26/04/23 9:30am

• rotor vap continued then house vaccuum.

28/04/23 9:30am

• NMR after 2 days house vacuum to check wetness MJE4-2.vac.pdf

11:10am

• TLC to check column conditions

  Details-

• Rf 5% EtOAc/Hex= 0.205
• Rf 10% EtOAc/Hex= 0.375
• 60% EtOAc/Hex= 0.205- streaking, nothing with triethylamine
• 40% EtOAc/Hex- 2 spots

2:30pm

• Ended up doing gradient of EtOAc/Hexane for column

01/05/23 9:30am

• TLC fractions 30% EtOAc/Hexane and TA- no spots except in fractions 2 and 3.

  

• Therefore ran column again with DCM and increasing amount of 10% MeOH in DCM

02/05/23 1:30am

• TLC in 5% MeOH in DCM as this is where UV peaked.

• combine fractions (also collect 1-3 fractions from first column)

08/05/23

• NMR All fractions: MJE4-2 fractions.pdf

Raw data: Fractions 1-3 from gradient column (labelled MJE4-2F) MJE4-2F_1.zip

Fractions from second column MeOH/DCM 5-7 MJE4-2(5)_1.zip 8-9 MJE4-2(8)_1.zip 11-16 MJE4-2(11)_1.zip

• MS of each compound that produced a peak on isolera. Fractions 1-3 from gradient column MJE4-2.1st.pdf 20230508-MJE4-2. 1st.zip

Fractions from second column MeOH/DCM 5-7 MJE4-2.5.pdf 20230508-MJE4-2.5.zip

8-9 MJE4-2.8.pdf 20230508-MJE4-2.8.zip

11-16 MJE4-2.11.pdf 20230508-MJE4-2.11.zip

[memm0740]

MJE4-3/4/5 Method

26/04/23 5pm

MJEa4-3W

1. Added benzenediamine (0.139g, 0.743mmol), water (6mL) to make slurry (stirred for 10min).
2. Then added thiourea (0.2718g, 1.31mmol). Started reflux at 5pm. Set temperature at 95C. Reaction continued temp-95C 26/04/23 till 9am on 01/05/23 (5d, 4hrs or total 124hrs)

MJE4-5M

1. Added benzenediamine (0.133g, 0.709 mmol), methanol (6mL) to make slurry (stirred for 10min).
2. Then added thiourea (0.2769g, 1.34mmol). Started reflux at 5pm. Set temperature at 75C. Reaction continued temp- 75C 26/04/23 till 9am on 01/05/23 (5d, 4hrs or total 124hrs)

MJE4-4A

1. Added benzenediamine (0.139g, 0.743mmol), water (6mL) and acetic acid to make slurry (stirred for 10min).
2. Then added thiourea (0.2645g, 1.28mmol). Started reflux at 5pm. Set temperature at 95C. Reaction continued temp-95C 26/04/23 till 9am on 01/05/23 (5d, 4hrs or total 124hrs)

27/04/23 9:55am

• TLC all in 5% EtOAc/Hex

Details- 3W- not as much thiourea and diamine, 5M- not done - still thiourea and diamine `but fading, 4A- slightly (negligible) more thiourea

27/04/23 4:15pm

• TLC all in 20% EtOAc/Hex

Details- 3W- less thiourea, potentially new spots for product?, 5M- less SM (see thiourea in both), 4A- less diamine, almost no thiourea

28/04/23 9:30am

• paused reflux
• TLC all in 20% EtOAc/Hex

Details- 3W- no SM, 5M- almost no thiourea, minimal diamine, 4A- no SM

28/04/23 12pm

• restarted reflux

01/05/23 12pm

• Mass spec all 3W MJE4-3W end reflux.pdf raw data- file too big

4A MJE4-4A end reflux.pdf 230501-MJE4-4A. end reflux.zip

5M MJE4-5M end reflux.pdf 230501-MJE4-5M.end reflux.zip

• TLC 30% EtOAc/Hexane all

  

  Details- no thiourea

  02/05/23 4:30pm

• NMR all 3 3W MJE4-W crude.pdf MJE4-3W.zip

4A MJE4-A crude.pdf MJE4-4A.zip

5M MJE4-M crude.pdf MJE4-5M.zip

-ANALYSIS- comparing MS and NMR to determine structure 3W (MS- 375 +1 and 199+1, 235-1)

• One methyl peak at 3.7 integrated at 1, no sulfur methyl peak around 2.43
• No aromatic peaks from diamine
• Shows potential aromatic peaks 7-8ppm for product

5M (MS- 398 +1)

• Tiny methyl peak at 2.43 from thiourea likely
• Seems like same 2 thiourea methyls
• No bromodiamine peaks
• Shows potential aromatic peaks 7-8ppm for product

4A (MS 581)

• Strong methyl peak at 3.68 integrated to be 1
• No bromodiamine peaks

• Shows potential aromatic peaks 7-8ppm for product

  04/05/23 2:30pm

  3. Work up reactions

MJE4-5M

• dissolve in 10mL diethyl ether and transfer to vial (15.7612g)
• left on house vac 4 days- 15.9601g

MJE4-3W vial (15.7641g)

• liquid-liquid extraction of 4-3W in DCM
• filtration, left on house vacuum overnight

MJE4-4A vial (15.7951g)

• filter and rinsed with diethyl ether, left on house vacuum overnight
• weight

08/05/23 4:30pm

• TLC column conditions 30% Eth/Hex no spot
• 5% Eth/Hex- no spot

09/05/23 9am

• TLC 20% Eth/Hex- no spots
• 90% DCM, 9% MeOH , 1% ammonia- none
• 60% Eth/Hex- none

Mass 5M- 15.9601g (0.1989g) 3W- 15.8156g (0.0515g) 4A- 15.9206g (0.1255g)

10/05/23 10am

• TLC 4A- fully dissolved in EtOAc/MeOH/Heat (polar to dissolve)
• run un 30% EtOAc/ Hex
• running in MeOH 2%- small spot
• MeOH 10%- moved up
• MeOH 10% with thiourea and bromodiamine- moved up

11/05/23 2pm

• MS 3W MJE4-3W.pdf 20230510-MJE4-3W.d.zip 20230511-MJE4-3W.crude2.zip

4A MJE4-4A.pdf 20230510_MJE4-4A.crude 2.zip

5M MJRE4-5M.pdf 20230510_MJE4-5M.crude2.zip

• NMR 3W MJE4-3W crude 2.pdf MJE4-3W_1.zip

4A MJE4-4A crude 2.pdf MJE4-4A_1.zip

5M MJE4-5M crude 2.pdf MJE4-5M_1.zip

12/05/23 2pm

• Final NMR - all reactions dried overnight house vacuum and ensured dissolved in EtOAc/MeOH MJE4-(3)(4)(5) concentrated.pdf

MJE4-3W_vac.zip MJE4-4A_vac.zip MJE4-5M_vac.zip

**%Yield

MJE4-4A- 0.0004646/0.0007463 x 100= 62%**

[memm0740]

Method MJE4-4A-1 15/05/23 9am

• Continuing to purify 4A (most promising results of product from MS and NMR)
• still dissolved from previous mixture
• TLC 10% EtOAC/Hex- stuck on base 30% E/H- streak 30% E/H with TA- stuck to baseline 40% with Goofy stain- no spots 60% with potassium permanganate- no spots

16/05/23 9am

• TLC 40% E/H with TA- streak/fade
• added DMF to fully dissolve 4A (started to be insoluble)
• TLC 10% E/H- stuck to base 10% MeoH/DCM- high Rf 10% MeoH/DCM with TA- no spots

17/05/23 11:15am

• Trying to spot 4A on TLC- retrying potential solvents with worked up crude product to try to spot
• 4A dissolve in EtOAc, NaHCO3- yellow ppt
• DMF, NaHCO3- yellow ppt
• added DCM to both- still not sol, white ppt
• added MeOH- still insol

4pm

• titrate with MeOH (based on work up from 4-6)
• wash solid x3 to rid impurities
• rotor vap and left on house vacuum

18/05/23 3:15pm

• troubleshooting TLC problem- 2D TLC in 30% E/H (spot and high vac)--> degraded
• TLC on alumina --> degraded
• TLC alumina 2% MeOH/DCM/1% NH4- ammonia to deal with slight acidity of Al (silica far ore acidic which could react with amines)d- disappears

22/05/23 9am

• NMR 4A and MeOH rinsings MJE4A.R.pdf MJE4A.18_1.zip MJE4a.R_1.zip

11:40am

• combine rinses to main product using DMF
• put under nitrogen to evaporate DMF

23/05/23 11:20am

• to remove DMF wash with toluene and rv x 3
• vial + product= 15.904gg

2pm

• NMR MJE4-4A-1.p1.pdf MJE4-4A-1.p1.zip

4:30pm

• toluene rinse and rv each time x3
• left on house vacuum overnight

24/05/23 9:30am

• NMR to check if any DMF left MJE4-4A-1.p2.pdf MJE4-4a-1.p2.zip

11:00am

• due to still DMF present rinse with toluene and rv x3
• left on house vacuum overnight to fully dry any remaining solvent

25/05/23 9:30am

• NMR to check purity and solvent levels MJE4-4A-1.p3.zip MJE4-4A-1.p3.pdf

• DMF at 2.88 and 2.98 still present despite another toluene rinse yesterday, presence of acetic acid at 2.10

26/05/23 2:00pm

• NMR more concentrated (5mg), in DMSO more soluble MJE4-4A-1.dmso 5mg.pdf MJE4-4A-1.dmso.zip

• put on high vacuum

[memm0740]

MJE4-4A-2 Method

22/05/23 1:00pm

1. Added benzenediamine (0.2806g, 1.50mmol), thiourea (0.5968g, 2.89mmol), deionised water (10mL) and glacial acetic acid (0.5mL) to make slurry (stirred for 10min).
2. Started reaction at 10:15am. Set temperature at 120C. Reaction started at 2:30pm, temp-95C. Reflux started at 4:30pm and temperature increased to 120C. Reaction continued temp-120C 22/05/23 till 9am on 19/04/23 (1d, 22hrs 36 minutes or total 46hrs)

23/05/23 9:30am

• Mass spec of reaction mixture MJE4-4A-2.pdf 20230523_MJE4-4A-2.crude.d.zip
• reaction not done, left at 85C overnight

24/05/23 9:30am

• Mass spec of reaction mixture MJE4-4A-2.crude2.pdf 20230524-MJE4-4A-2.crude2.d.zip
• product peak plus H noted at 270 (+1)

1:00pm

• reflux stopped and reaction worked up
• using two lit sources (patent from MJE4-1 and paper for MJE4-5M) tested solubility in diethyl ether and MeOH for work up
• much less soluble in diethyl ether so chosen for work up
• however rinsed equipment with MeOH into vial to get highest yield
• vial left on house vacuum overnight
• vial= 15.2814g vial + product= 15.5963g *%yield=0.001171 (prod)/0.0015 (lim) 100= 78%**

25/05/23 2:30pm

• NMR to check purity MJE4-4A-2.post work-up.pdf MJE4-4A-2.post work-up.zip

• differences from MJE4-4A-1 : no acetic acid, no DMF peaks (none was added), no peak at 3.79

26/05/23 2:00pm

• NMR more concentrated (5mg), in DMSO more soluble MJE4-4A-2.dmso 5mg.pdf MJE4-4A-2.dmso.zip

• put on high vacuum

• NMR rinses MJE4-4A-2.rinses.pdf MJE4-4A-2.R_1.zip Note- discarded as did not match product peaks.

[memm0740]

MJE4-4A-3 Method

09/06/23 10am

1. Added benzenediamine (0.307g, mmol), thiourea (0.7396g, mmol), deionised water (10mL) and glacial acetic acid (0.5mL) to make slurry (stirred for 10min).
2. Started reaction at 5:15pm. Set temperature at 120C. Reaction continued temp-120C 12/06/23 till 10am on 19/04/23 (2 days, 16 hours, 45 minutes or total 64hrs)

12/06/23 10:30am

• Mass spec 20230612_MJE4-4A-3.crude.pdf 20230612_MJE4-4A-3.crude1.d.zip Note- almost identical to 4A-2 MS after reaction. Product at 270 (+1 H).

• TLC- to check if SM gone (this product does not TLC well) -dissolve SM and RM in EtOAc/MeOH/heat- worked for RM

• TLC in 40% E/H- RM streak, no thiourea, possibly bromo compound

  

11:30am

3. work up following 4A-2
   • rinse with 9mL diethyl ether- dry on vacuum filtration around 3 hours

4pm

• rinsed into vial with MeOH vial= 15.6880g

5:15pm

• left on high vacuum overnight

13/06/23 10am

• vial + product= 16.177g yield= n(product) = 0.489/269= 0.00181moles n(limiting)= 0.307/186= 0.00165moles 0.00181/0.00165 * 100= 110% - not all product

19/06/23 12:00pm -NMR in dmso MJE4-4A-3 dry 1.pdf MJE4A-3_1.zip

Note- 3 doublet pairs each integrating to approximately 1, which satisfies Hs on benzene. Peak at 3.75, intergrates to 3.21 which satisfies the the methyl peak on on the carbamate end. Amine peaks were not visible.

[memm0740]

MJE4-4A-4 Method

03/08/23 11:45am

1. Added benzenediamine (0.500g, 0.00267mmol), thiourea (1.37505g, 0.006645mmol), deionised water (10mL) and glacial acetic acid (0.5mL) to make slurry (stirred for 10min).
2. Started reaction. Set temperature at 90C. Reaction continued temp-90C 03/08/23 till 10am on 04/08/23 5pm. Restarted 07/08/23

3:20pm -dissolved diamine, thiourea, RM in MeOH (completely soluble)

• TLC

4:45pm

• MS- small 269 peak 230803_MJE4a-4.crude1.pdf 230803_MJE4a-4.crude 1.zip

04/08/23

• MS- 268 -1 larger peak 230804_MJE4a-4.crude2.pdf 230804_MJE4a-4.crude2.d.zip

11:30am TLC- potentially diamine still present.

07/08/23

• turned back on

3:30pm

• TLC 9%MeOH/90% DCM/1%NH4
• TLC5%MeOH/95% DCM- reaction mst likely done, presence of thiourea

5pm MS- reaction done (no presence of starting material, so can work up) 230807_MJE4a-4.crude3.pdf 230807_MJE4a-4.crude3.d.zip

08/08/23 9am

• Work up
• vacuum filtration and rinse with diethyl ether- works well
• dried on vacuum for approx 2hours

12:30pm

• solid does not dissolve in deuterated methanol, acetonitrile or acetone. Must use DMSO.
• vial= 15.9983g
• put solid under vacuum and tipped out filtrate
• NMR of solid 4a-4.vac.pdf MJE4a-4_1.zip

Note- Note- 3 doublet pairs each integrating to approximately 1, which satisfies Hs on benzene. Peak at 3.75, integrates to 3.21 which satisfies the the methyl peak on on the carbamate end. Amine peaks were not visible. Large water peak.

12:45pm

• MS Solid 230808_MJE4a-4.solid.pdf 230808_MJE4a-4.solid.d.zip

Filtrate 230808_MJE4a-4.filtrate.pdf 230808_MJE4a-4.filtrate.d.zip Note- no 269 peak in filtrate. 268 in solid MS but not only compound.

16/08/23

• vial + product= 16.6988g
• %yield= 0.002604/0.00267 x 100= 97.53% (crude))

18/08/23

• MS after dried over few days 230818_MJE4a-4dry.pdf 230818_MJE4a-4dry.d.zip

Note- doublet peak at 236??

• NMR MJE4a-4.dry.pdf mje4A-4.DRY_1 (1).zip

Note- Note- 3 doublet pairs each integrating to approximately 1, which satisfies Hs on benzene. Peak at 3.75, integrates to 3.23 which satisfies the the methyl peak on on the carbamate end. Amine peaks were not visible. Large water peak.

21/08/23 10am

• plan to purify
• trying to dissolve:
• EtOAc/MeOH- partial
• DCM/MeOH- partial
• H2O- no
• H2O/ethanol- no
• DMF- yes

28/08/23 3pm

• qNMR - 96% purity
• good enough to continue to next step

[memm0740]

MJE4-4A-5 (Scale up) Method

19/09/23 9am

1. Added benzenediamine (2.053g, 10.6mmol), deionised water (53mL), acetic acid (2.65mL). Switched on stirring 9:37am.
2. Added thiourea (4g, 19.4mmol), Switched on 9:50am. Set temperature at 90C.
3. Reflux started at 11:16am (hotplate not working). Reaction continued temp-90C 19/09/23 till 11am on 20/09/23 2pm. Notes- was ppt out of water immediately

20/09/23

• Reaction still ppt out of solution -pale purple brown
• TLC 5%MeOH/DCM

10am

• MS - 268 is present
• NMR MJE4a-5.crude 1_1.zip 4a-5.crude1.pdf Note- looks like product formed

4:30pm

4. Work up- vac filtration, rinse with diethyl ether.

5pm

• put into vial

21/09/23 10am

• put vial on hivac
• NMR (to check product) MJE4A-5.DRY_1.zip 4a-5.dry1.pdf

4:15pm

• mass 1.81g
• NMR to check if dry enough to do carbamate cleavage MJE4a-5.dry2_1.zip 4a-5.dry2.pdf
• Note- needs to dry further.

[memm0740]

NMR starting materials 19/09/23 11am MJEdiamine_2.zip thiourea 2.pdf Note- the peak that was being shown at 3.69 is most likely an impurity from the thiorea. This peak goes away once carbamate cleaved in MJE9.

MJEthiourea_2.zip diamine 2.pdf Note- looks quite clean