1

Supporting Information

Accelerated Microdroplet Synthesis of Benzimidazoles by

Nucleophilic Addition to Protonated Carboxylic Acids

Pallab Basuri,a L. Edwin Gonzalez,b Nicolás M. Morato,b Thalappil Pradeep*a and R. Graham Cooks*b

a DST Unit of Nanoscience (DST UNS), Thematic Unit of Excellence (TUE), Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.b Aston Labs, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA*Corresponding authors

Electronic Supplementary Material (ESI) for Chemical Science.This journal is © The Royal Society of Chemistry 2020

2

Table of ContentsFigure S1 ................................................................................................03Figure S2 ................................................................................................04Figure S3 ................................................................................................05Figure S4 ................................................................................................06Figure S5 ................................................................................................07Figure S6 ................................................................................................08Figure S7 ................................................................................................09Figure S8 ................................................................................................10Figure S9 ................................................................................................11Figure S10 ..............................................................................................12Figure S11 ..............................................................................................13Figure S12 ..............................................................................................14Figure S13 ..............................................................................................15Figure S14 ..............................................................................................16Figure S15 ..............................................................................................17Figure S16..............................................................................................18Figure S17..............................................................................................19Figure S18 ..............................................................................................20Figure S19 ..............................................................................................21Figure S20 ..............................................................................................22Figure S21 ..............................................................................................23Figure S22 ..............................................................................................24Figure S23 ..............................................................................................25Figure S24 ..............................................................................................26Figure S25 ..............................................................................................27Figure S26 ..............................................................................................28Figure S27 ..............................................................................................29Figure S28 ..............................................................................................30Figure S29 ..............................................................................................31Figure S30 ..............................................................................................32Figure S31 ..............................................................................................33Figure S32 ..............................................................................................34Figure S33 ..............................................................................................35Figure S34 ..............................................................................................36Figure S35 ..............................................................................................37Figure S36 ..............................................................................................38Figure S37 ..............................................................................................39Figure S38 ..............................................................................................40Figure S39 ..............................................................................................41Figure S40 ..............................................................................................42Figure S41 ..............................................................................................43Figure S42 ..............................................................................................44Figure S43 ..............................................................................................45Figure S44 ..............................................................................................46Figure S45 ..............................................................................................47Figure S46 ..............................................................................................48

3

Figure S1. MS/MS spectra of (a) reagent peak at m/z 109, (b) product peak at m/z 119, and (c) intermediate peak at m/z 137 for nESI microdroplet synthesis in methanol.

4

Figure S2. Mass spectra of benzimidazole standard. (a) Mass spectrum of 1 mM solution of benzimidazole in methanol. Inset shows the isotopic distribution of the peak. (b) MS/MS spectrum of protonated benzimidazole at m/z 119.

5

Figure S3. Microdroplet synthesis of 2-methylbenzimidazole. (a) Mass spectrum of the reaction mixture containing phenylenediamine (PDA) and acetic acid in methanol. The final concentration of the individual reagents is 8 mM. (b) MS/MS spectrum of the product at m/z 133 (c) MS/MS spectrum of intermediate at m/z 151.

6

Figure S4. Mass spectra of 2-methylbenzimidazole standard. (a) Mass spectrum of 1 mM solution of 2-methylbenzimidazole in methanol. Inset shows the isotopic distribution.( b) MS/MS spectrum of protonated 2-methylbenzimidazole at m/z 133.

7

Wavelength (nm)

Abso

rban

ce

220 240 260 280 3000.0

0.5

1.0 PDA PDA + FA Benzimidazole

Figure S5. UV-vis spectra of o-phenylenediamine (black), reaction mixture for the synthesis of benzimidazole (red) and standard product (blue), all in methanol. The shift in the UV-vis spectra, as indicated by dotted lines, is due to the addition of formic acid and corresponds to Brønsted acid formation in solution by addition of a proton.

8

Figure S6. 1H NMR data (400 MHz, CDCl3) for o-phenylenediamine in CDCl3. (. δ 6.71 (s, 1H), 3.49 – 3.23 (m, 1H). Solvent peak is observed at 7.26 ppm.

9

Figure S7. 1H NMR data (400 MHz, CDCl3) for formic acid. δ 10.90 (s, 1H), 8.04 (s, 1H). Solvent peak is observed at 7.26 ppm.

10

Figure S8. 1H NMR data (400 MHz, CDCl3) for a mixture of o-phenylenediamine and formic acid. δ 8.02 (s, 1H), 6.79 – 6.69 (m, 5H), 4.61 (s, 7H). Solvent peak is observed at 7.26 ppm.

11

Figure S9. 1H NMR data (400 MHz, CDCl3) for benzimidazole standard. δ 8.08 (s, 1H), 7.71 – 7.64 (m, 2H), 7.31 (dt, J = 6.1, 3.6 Hz, 2H). Solvent peak is observed at 7.26 ppm.

12

Figure S10. UV-vis spectra of o-phenylenediamine (black), its mixture with acetic acid (green) and standard 2-methylbenzimidazole (violet) in methanol.

220 240 260 280 3000.0

0.5

1.0 PDA PDA + AA 2-Methylbenzimidazole

Wavelength (nm)

Abso

rban

ce

13

Figure S11. 1H NMR data (400 MHz, CDCl3) for o-phenylenediamine standard. δ 6.69 (dd, J = 5.7, 3.5 Hz, 1H), 6.58 (dd, J = 5.8, 3.4 Hz, 1H).

14

Figure S12. 1H NMR data for acetic acid(400 MHz, MeOD) δ 1.98 (s, 1H). Peaks at 4.85 ppm and 3.30 ppm are solvent peaks.

15

Figure S13. 1H NMR data for mixture of o-phenylenediamine and acetic acid (400 MHz, MeOD) δ 6.69 (dq, J = 6.4, 3.6, 3.0 Hz, 1H), 6.59 (dt, J = 5.8, 2.8 Hz, 1H), 1.98 (s, 1H). Peaks at 4.85 ppm and 3.30 ppm are due to solvent.

16

Figure S14. 1H NMR data (400 MHz, MeOD) for 2-methylbenzimidazole standard. δ 7.51 – 7.37 (m, 1H), 7.16 (dd, J = 6.0, 3.2 Hz, 1H), 2.55 (s, 2H). Peaks at 4.85 ppm and 3.30 ppm are due to solvent.

17

Figure S15. Temperature dependent mass spectra for microdroplet synthesis in methanol of a) benzimidazole and b) 2-methylbenzimidazole. The reagent peak at m/z 109, as indicated by yellow shading, decreases with increasing temperature, whereas, the product peaks at m/z 119 and m/z 133, as indicated by green shading, increase with increasing temperature.

18

Figure S16. Conversion ratio versus temperature plot for the intermediate (m/z 137) in benzimidazole synthesis in methanol microdroplets. Inset shows the equation for conversion ratio.

19

Figure S17. Mass spectra of reaction mixtures containing (a) o-phenylenediamine and formic acid (b) trifluoroacetic acid and (c) MS/MS spectrum of protonated trifluoroacetic acid. Zoom-in view of selected mass ranges in (a) and (b) showing peaks corresponding to protonated formic acid and trifluoroacetic acid. The solutions were prepared in HPLC grade methanol at 8 mM concentration.

20

Figure S18. Isotope labeling experiments. Mass spectra showing reaction mixture for microdroplet reaction of phenylenediamine with (a) deuterated formic acid (DCOOH) and (b) acetic acid (CD3COOH). The isotopically labeled product peaks are indicated with stars. The solvent used for the reaction is deuterated methanol. The temperature of the inlet was set to 50 oC for these experiments.

21

Figure S19. Ratio of product ion to reagent ion intensity for ambient thin film synthesis in methanol containing traces of p-toluenesulfonic acid to increase the lifetime of the fluid state for (a) benzimidazole and (b) 2-methylbenzimidazole. c) Schematic illustration of the thin film experiments from Z. Wei, M. Wleklinski, C. Ferreira and R. G. Cooks, Angewandte Chemie International Edition, 2017, 56, 9386-9390. Note the induction period of some minutes while the methanol evaporates.

a)

b)

c)

22

0

50

100

0

50

100

0

50

100

0

50

100

100 120 140 160 180 2000

50

100

1% water1% water

3% water

10% water

30% water

50% water

3% water

10% water

30% water

50% water

m/z

Nor

mal

ized

inte

nsity

(a.u

.)IP+I/IR = 62%

IP+I/IR = 95%

IP+I/IR = 68%

IP+I/IR = 52%

IP+I/IR = 54%109

119 13

7

Figure S20. Benzimidazole reaction in presence of macroscopic amounts of water in methanol monitored by relative intensity of the product ion m/z 117 plus the intermediate ion m/z 137 vs. that of the reagent ion m/z 109. As the water concentration is increased up to 10%, we see increased product and intermediate formation. Above this concentration the relative product and intermediate intensities fall.

23

50 100 150 200 2500

50

100

B

SPECTRUM - MS (Exp 4 dry acn_1.raw)

Nor

mal

ized

inte

nsity

(a.u

.)

m/z

109

Figure S21. Benzimidazole reaction in dry ACN. Note the low signal (noise) and the absence of both product and intermediate ion signals. Other than the reagent signal, the peaks seen in the mass spectrum are from background.

24

Figure S22. Mass spectrum of o-phenylenediamine/formic acid mixture in methanol in the presence of HCl. Concentrations of reactants and of HCl were 8 mM. Similar CRs were observed with and without HCl.

25

Figure S23. Product to reagent ion intensity ratio for the bulk reaction in methanol under ambient conditions for 2-methylbenzimidazole synthesis. Inset shows the molecular structure of the product. The starting concentration of each reagent in methanol was e 8 mM. The reaction was performed in a closed 500 mL round bottom flask and MS analysis was done using 50 oC inlet temperature to avoid reaction acceleration during bulk product analysis.

0 900 1800 2700

0.3

0.6

0.9

1.2

1.5

(I P/I R

)X10

0

Time (min)

NH

NCH3

26

0

50

100

50 100 150 2000

50

100

B Bulk 24 hrReaction temperature 200 oC

Microdroplet synthesis Inlet temperature 200 oC

DR

elat

ive

inte

nsity

m/z

Rel

ativ

e in

tens

ity 109

133

H3C OH

OHN

NCH3

NH2

NH2

+

a) b)

X108

Appa

rent

acc

eler

atio

n fa

ctor

Temperature of the mass spec inlet (oC)50 100 150 200 250 300 350

01234567

Under methanol reflux

Figure S24. Effect of inlet temperature on accelerated formation of 2-methylbenzimidzaole (m/z 133) from phenylenediamine (m/z 109). (a) Comparison of mass spectrum of bulk reaction mixture after 24 h under methanol reflux with that for microdroplet synthesis at 200 oC inlet temperature. (b) Temperature of MS inlet vs. apparent reaction rate acceleration factor. Inset shows the reaction scheme. Apparent acceleration factor considered the difference in reaction time of the droplet and bulk reactions. Note that the bulk reaction analysis was performed at constant 50 oC inlet temperature to avoid reaction acceleration during the analysis.

27

Figure S25. Mass spectrum of the isolated product after benzimidazole synthesis in methanol by spray deposition with a diagram that depicts the spray deposition reaction setup. The crude mixture was separated using flash column chromatography. Yield was determined to be about 72%.

kV

50 100 150 200 2500

1M

2M

3M

NH

NH

m/z

Abso

lute

inte

nsity

119

28

Figure S26. 1H NMR (400 MHz, CDCl3) of the isolated product from the deposited sample in benzimidazole spray deposition synthesis. δ 8.24 (s, 1H), 8.10 (s, 6H), 7.68 (dd, J = 6.1, 3.2 Hz, 11H), 7.31 (dd, J = 6.1, 3.2 Hz, 11H), 7.26 (s, 18H), 1.25 (s, 5H). Peak at 7.26ppm is the solvent peak and 8.24ppm peak is an impurity.

29

Figure S27. Mass spectrum of the isolated product of the deposited sample for the 2-benzimidazole spray synthesis. Low isolated yield resulted in noise in the mass spectrum.

50 100 150 200 250 3000

23k

46k

69kA

bsol

ute

ion

inte

nsity

(a.u

.)

m/z

NH

NCH3

133

30

Figure S28. 1H NMR (400 MHz, MeOD) for the isolated product of the deposited sample from the 2-methylbenzimidazole spray synthesis. δ 7.96 – 7.91 (m, 2H), 7.65 – 7.58 (m, 1H), 7.02 (s, 2H), 2.55 (s, 1H). Peaks at 4.85 and 3.29-3.31ppm are solvent peaks while other minor peaks are from impurities.

31

Figure S29. (a) Online mass spectrum of microdroplet reaction between o-phenylenediamine and trifluoroacetic acid in methanol at 50 oC inlet temperature. The MS/MS spectrum of the (b) product and (c) intermediate are shown. The reagent and the product are denoted as R and P.

32

Figure S30. a) Online MS of microdroplet reaction between o-phenylenediamine and propanoic acid in methanol at 50 oC inlet temperature. The MS/MS spectrum of the (b) product and (c) intermediate are shown. The reagent and the product are denoted as R and P.

33

Figure S31. (a) Online MS of microdroplet reaction between o-phenylenediamine and benzoic acid in methanol at 50 oC inlet temperature. The MS/MS spectrum of (b) product and (c) intermediate are shown. The reagent and the product are denoted as R and P.

34

Figure S32. (a) Online MS of microdroplet reaction between 4-methyl-1,2-phenylenediamine and formic acid in methanol at 50 oC inlet temperature. MS/MS spectrum of the (b) reagent, (c) product, and (d) intermediate. The reagent and the product are denoted as R and P.

35

Figure S33. (a) Online MS of microdroplet reaction between 4,5-dimethy-o-phenylenediamine and formic acid in methanol at 50 oC inlet temperature. MS/MS spectra of the (b) reagent (c) product and (d) intermediate. The reagent and the product are denoted as R and P.

36

Figure S34. Online MS of microdroplet reaction between 4-nitro-1,2-phenylenediamine and formic acid in methanol at 50 oC inlet temperature. No product formation observed. The reagent is denoted as R.

H OH

OHN

N

NH2

NH2

+O2N O2N

100 150 200 250 3000

50

100

m/z

Rel

ativ

e in

tens

ity

No product

154 [R+H]+

37

Figure S35. (a) Online MS of microdroplet reaction between 4-chloro-1,2-phenylenediamine and formic acid in methanol at 50 oC inlet temperature. MS/MS spectrum of (b) product and (c) intermediate. The reagent and the product are denoted as R and P.

38

Figure S36. (a) Online MS of microdroplet reaction between 4-methoxy-1,2-phenylenediamine and formic acid in methanol at 50 oC inlet temperature. The fragmentation pattern of (b) reagent (c) product and (d) intermediate. The reagent and the product are denoted as R and P.

39

Figure S37. (a) Online MS of microdroplet reaction between 1,2-diaminonapthalene and formic acid in methanol at 50 oC inlet temperature. The MS/MS spectra of (b) reagent (c) product and (d) intermediate. The reagent and the product are denoted as R and P.

40

Figure S38. Characterization of isolated product of spray deposition reaction between trifluoroacetic acid and o-phenylenediamine. (a) Mass spectrum and (b) 1H NMR (400 MHz, MeOD) of the product. δ 7.69 (dd, J = 6.2, 3.2 Hz, 1H), 7.40 (dd, J = 6.3, 3.2 Hz, 1H). Peaks 4.85ppm and 3.28-3.30ppm are solvent peaks.

41

Figure S39. Characterization of isolated product of the spray deposition reaction between propanoic acid and o-phenylenediamine in methanol. Due to poor separation, an NMR of the isolated product was not obtained.

42

Figure S40. Characterization of isolated product of spray deposition reaction between formic acid and 4-methy-1,2-phenylenediamine. (a) Mass spectrum and (b) 1H NMR (400 MHz, CDCl3) spectrum of the product. δ 8.08 (s, 1H), 7.55 (d, J = 8.3 Hz, 1H), 2.47 (s, 3H). Peak in 7.26ppm region is the solvent peak. Other peaks are due to artifacts or by-products.

43

Figure S41. Characterization of the isolated product of spray deposition reaction between formic acid and 4,5-dimethyl-1,2-phenylenediamine in methanol. a) Mass spectrum and b) 1H NMR (400 MHz, CDCl3) δ 8.37 (s, 1H), 7.41 (s, 2H), 2.32 (s, 6H). Peak in 7.26 ppm region is the solvent peak. Unlabeled peaks represent minor reaction products.

44

Figure S42. Characterization of isolated product of spray deposition reaction between formic acid and 4-chloro-1,2-phenylenediamine in methanol. (a) Mass spectrum and (b) 1H NMR (400 MHz, MeOD). δ 8.19 (s, 1H), 7.60 (s, 1H), 7.57 (d, J = 8.7 Hz, 1H), 7.25 (dd, J = 8.5, 2.0 Hz, 1H). Peaks 4.85ppm and 3.29-3.31ppm are solvent peaks.

45

Figure S43. Characterization of isolated product of spray deposition reaction between formic acid and 4-methoxy-1,2-phenylenediamine in methanol. a) Mass spectrum and b) 1H NMR (400 MHz, MeOD). δ 9.24 (s, 1H), 7.71 (d, J = 9.0 Hz, 1H), 7.31 – 7.17 (m, 2H), 3.91 (s, 3H). Peaks 4.85ppm and 3.29-3.31ppm are solvent peaks.

46

Figure S44. Characterization of isolated product of spray deposition reaction between formic acid and 1,2-diaminonapthalene in methanol. (a) Mass spectrum and (b) 1H NMR (400 MHz, MeOD). δ 8.39 (d, J = 8.2 Hz, 1H), 8.25 (s, 1H), 8.18 (s, 1H), 7.96 (d, J = 8.2 Hz, 1H), 7.71 (d, J = 1.5 Hz, 2H), 7.60 (t, J = 7.7 Hz, 1H), 7.49 (t, J = 7.6 Hz, 1H). Peaks 4.85ppm and 3.29-3.31ppm are solvent peaks.

47

Figure S45. Kinetics data for thin film reactions. Reactions were done for 6 h in methanol under ambient conditions. Lines are drawn only as guides.

0 100 200 300 400

0

20

40

60

(I P/I R

)X10

0

Time (min)

0 100 200 300 400

0

40

80

120

160

(I P/I R

)X10

0

Time (min)

0 100 200 300 400

0

40

80

120(I P

/I R)X

100

Time (min)

0 100 200 300 400

0

20

40

(I P/I R

)X10

0

Time (min)

0 100 200 300 4000

20

40

60

(I P/I R

)X10

0

Time (min)

0 100 200 300 4000

4

8

12

(I P/I R

)X10

0

Time (min)

0 100 200 300 4000

2

4

(I P/I R

)X10

0Time (min)

0 100 200 300 400

0.0

0.4

0.8

1.2

(I P/I R

)X10

0

Time (min)

No reaction

0 100 200 300 4000.0

0.2

0.4

0.6

(I P/I R

)X10

0

Time (min)

0 50 100 150 200

0

2

4

(I P/I R

)X10

0

Time (min)

NH

NCF3

NH

NCH2CH3

NH

NPh

NH

NCH2Ph

NH

NH

H3C

NH

NH

H3C

H3C

NH

NH

O2N

NH

NH

Cl

NH

NH

H3CO

NH

NH

48

Figure S46. Kinetics data for bulk reactions. Reactions were done for 41 h in methanol under ambient conditions. Lines are drawn only as guides.

0 900 1800 2700

0

1

2

3

(I P/I R

)X10

0

Time (min)

0 400 800 12000.0

0.2

0.4

0.6

0.8

(I P/I R

)X10

0

Time (min)

0 900 1800 2700

0.0

0.6

1.2

1.8

2.4

(I P/I R

)X10

0

Time (min)

0 400 800 12000.00

0.07

0.14

0.21

(I P/I R

)X10

0

Time (min)

0 400 800 1200

0.0

0.5

1.0

1.5

2.0

(I P/I R

)X10

0

Time (min)

0 800 1600 24000

1

2

3

(I P/I R

)X10

0

Time (min)

0 900 1800 27000.0

0.4

0.8

1.2

(I P/I R

)X10

0

Time (min)

0 300 600 900

0.0

0.8

1.6

2.4(I P

/I R)X

100

Time (min)

0 900 1800 2700

0

10

20

30

(I P/I R

)X10

0

Time (min)

0 900 1800 2700

0

35

70

105

(I P/I R

)X10

0

Time (min)

NH

NH

NH

NCF3

NH

NCH2CH3

NH

NPh

NH

NCH2Ph

NH

NH

H3C

NH

NH

H3C

H3C

NH

NH

Cl

NH

NH

H3CO

NH

NH