Supporting Information

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1 Supporting Information Continuous Flow Process for Reductive Deoxygenation of ω-chloroketone in the Synthesis of Vilazodone Avedis Karadeolian, Dineshkumar Patel, Prabhudas Bodhuri*, Gamini Weeratunga, and Boris Gorin Division of Research and Technology, Apotex Pharmachem Inc., 34 Spalding Drive, Brantford, Ontario, N3T 6B8, Canada * Corresponding Author. pbodhuri@apotexpharmachem.com; Telephone: (519) Table of Contents Material and General Considerations... 2 Continuous Flow Chemistry Equipment... 2 Experimental... 4 NaBH 4 in tetraglyme reductive deoxygenation of 2b... 4 Procedure... 5 BH 3 THF reductive deoxygenation of 2b in ACR P Procedure BH 3 THF reductive deoxygenation of 2b in three jacketed CSTRs Procedure: S1

2 Material and general considerations All manipulations of air- and moisture-sensitive substances were carried out using inert conditions with nitrogen gas. Tetraglyme, iron trichloride, sodium borohydride and borane THF solution were purchased from Sigma Aldrich and used as is. THF was obtained from our plant with a KF <0.5% and used as is. Diglyme was purchased from Sigma Aldrich and was 99.97% by GC. Compound 5 was provided by our Apotex Pharmachem Inc. Signa S.A. de C.V., Toluca, Mexico branch. HPLC analysis conducted using Waters 2695 Separations Module with an X- Bridge C18, 4.6 X 150 mm, 3.5 μm column, and processed with relative area % values. LC/MS obtained using Agilant Technologies 1200 Series HPLC and Agilant Technologies 6510 Q-TOF LC/MS. Continuous Flow Chemistry Equipment Coflore Agitated Cell Reactor P200 (Coflore ACR P200) was purchased from AM Technology (Figure S1) Unit 18, Berkeley Court, Manor Park Runcorn, Cheshire, WA7 1TQ Telephone +44 (0) Website: Peristaltic pumps were purchased from Cole-Parmer and consisted of Masterflex L/S Digital Miniflex Pump, Dual-Channel, 300 RPM, 115/230 VAC , model number RK Peristaltic pump tubing was purchased from Cole-Parmer and consisted of Masterflex Chem-Durance Bio Pump Tubing, L/S 16, item# RK Transfer tubbing consisted of Cole-Parmer PTFE Tubing, 1/16"ID x 1/8"OD, item # RK The ACR P200 reactor block was heated via Julabo FP40-HE refrigerated/heating unit filled with silicon oil. S2

3 a) b) Figure S1: a) ACR P200 instrument; b) Reactor block with numbered CSTRs S3

4 Experimental NaBH4 in tetraglyme reductive deoxygenation of 2b Preparation of a suspension of 2b in THF: A 100 ml round bottomed flask was charged with 2b (20 g, mmol) and THF (68 ml) and stirred at C gently to avoid splatter on the flask walls. Total suspension volume was 85 ml. Preparation of FeCl 3 solution in THF: A100 ml 2 necked round bottomed flask was charged with THF (56 ml), the headspace was purged with nitrogen gas and FeCl 3 (14.47 g, mmol, 1.1 eq) was added slowly through a solids addition apparatus under nitrogen gas. The addition is exothermic and the rate was adjusted to maintain a solution temperature of <30 C. This solution was then transferred via cannula to a conical flask. Total volume of the green solution was 78 ml. Preparation of NaBH 4 solution in tetraglyme: A 100 ml round bottomed flask was charged with NaBH 4 (4.60 g, mmol, 1.5 eq) and tetraglyme (60 ml) and stirred at C until a homogenous solution was obtained (total volume of 65 ml). This solution was split into two portions with 4:11 ratio to obtain 17.3 ml (for pumping into CSTR 6) and 47.7 ml (for pumping into CSTR 2) solution respectively. When the solution was split into two portions they were transferred into conical flasks. Total reaction volume: The total void volume of the reaction block is 62 ml (10 CSTR s x 10 ml each 4 x 5 ml agitators 6 x 3 ml agitators = 62 ml) but from previous experience we calculated that of the 62 ml only 65% of that volume is occupied by liquid while the rest is occupied by hydrogen gas liberated during the reaction. This provides a total reaction volume of 40.3 ml for which we used to calculated our total flow rate and residence time of 30 minutes. Table S1: Solution/slurry flow rates: Solution Total volume (ml) Flow rate (ml/minute) 2b in THF FeCl 3 in THF NaBH 4 in tetraglyme for CSTR NaBH 4 in tetraglyme for CSTR Total S4

5 Procedure Once all the feed suspension/solutions were prepared they were connected to the appropriate tubing as shown in Figure S2 and Figure S3 and placed under a nitrogen atmosphere. The reactor block was heated to 40 C via circulation of silicon oil from a Julabo heating unit. The four lines were primed with suspension/solutions and then the suspension of 2b (20 g, mmol, in 68 ml THF) and FeCl 3 solution (14.47 g, mmol, 1.1 eq., in 56 ml THF) were simultaneously pumped into CSTR 1. Once this mixture begins to enter CSTR 2 the main solution of NaBH 4 in tetraglyme (3.37 g, mmol, 1.1 eq., in 44 ml tetraglyme) was pumped into the reaction block at which point hydrogen gas evolution begins and the suspension becomes an orange/green solution. When this solution starts to enter CSTR 6 the second solution of NaBH 4 in tetraglyme (1.23 g, mmol, 0.4 eq., in 16 ml tetraglyme) was pumped into the reaction block. The reaction mixture was transferred from the top of the reaction block into a flask containing aqueous citric acid (7.79 g, mmol, 0.5 eq., in 60 ml water). The hydrogen gas accumulated in this flask is safely diluted with nitrogen gas (below 4 vol. % H 2 in the mixture as per ISO standard) and was released into the atmosphere. When all suspension 2b was added into the reactor block the flask was rinsed with 10 ml THF and pumped into the reactor to quantify the transfer of 2b. At this point all the reagent flasks were changed to flasks containing THF and continue to pump at their original flow rates for an additional 30 minutes while collecting reaction mixture in the receiving flask. This biphasic solution was concentrated to remove THF then diluted with n-buoh (60 ml), water (40 ml) and the phases were separated. The organic phase was washed three times with water (40 ml), diluted with n-buoh (40 ml) and concentrated to 40 ml. The solution was diluted once more with n-buoh (60 ml) and concentrated to 40 ml at which time some solids precipitate. The suspension was charged with 34-37% aqueous HCl (8.19 g, mmol, 1 eq.), heated to 65 C for 3 hours then slowly cooled to C and maintained at that temperature for hours. The suspension was filtered at C, washed with 10 ml cold (-10 to -5 C) n-buoh then dried under vacuum to provide 6.80 g (45.6%) of 3b with an HPLC purity of a% (Figure S4) (impurity 5 retention time of minutes). Proton NMR data of 3b: 1 H-NMR (DMSO-d6): δ (ppm) 11.41(br s, 1H), 8.09 (s, 1H), 7.52 (d, 1H, J = 8.4 Hz), 7.42 (dd, 1H, J = 1.5 Hz and J = 8.4 Hz), 7.35 (d, 1H, J = 1.7 Hz), 3.68 (m, 2H), 2.75 (m, 2H), 1.77 (m, 4H). S5

6 Agitators: CSTRs 1 to 4 contain 50 vol% agitators and CSTRs 5 to 10 contain 30 vol% agitators for a total void volume of about 62 ml Figure S2: Schematic of ACRP200 reaction block for NaBH 4 in tetraglyme continuous flow process for the reductive deoxygenation of 2b S6

7 Figure S3: Set-up of ACR P200 for NaBH 4 in tetraglyme continuous flow process for the reductive deoxygenation of 2b S7

8 Figure S4: HPLC chromatogram of 3b obtained after NaBH 4 reduction of 2b in ACR P200 S8

9 BH3 THF reductive deoxygenation of 2b in ACR P200 Preparation of a suspension of 2b in THF: A 100 ml round bottomed flask was charged with 2b (20 g, mmol) and THF (73 ml) and stirred at C gently to avoid splatter on the flask walls. Total suspension volume was 85 ml. Preparation of FeCl 3 solution in THF: A100 ml 2 necked round bottomed flask was charged with THF (68 ml), the headspace was purged with nitrogen gas and FeCl 3 (13.15 g, mmol, 1 eq) was added slowly through a solids addition apparatus under nitrogen gas. The addition is exothermic and the rate was adjusted to maintain a solution temperature of <30 C. This solution was then transferred via cannula to a conical flask. Total volume of the green solution was 70 ml. BH 3 THF was purchased from Sigma-Aldrich as a 1 M solution in THF (item # ML) and used as is. One equivalent (81.09 mmol, 81 ml) of BH 3 THF was charged into the reactor from CSTR 2 and 0.2 eq. (16.22 mmol, 16 ml) was charged from CSTR 6. The feed flasks for these solutions were conical in shape. Total reaction volume: The total void volume of the reaction block is 62 ml (10 CSTR s x 10 ml each 4 x 5 ml agitators 6 x 3 ml agitators = 62 ml) but from previous experience we calculated that of the 62 ml only 65% of that volume is occupied by liquid while the rest is occupied by hydrogen gas liberated during the reaction. This provides a total reaction volume of 40.3 ml for which we used to calculated our total flow rate and residence time of 5-6 minutes. Table S2: Solution/slurry flow rates: Solution Total volume (ml) Flow rate (ml/minute) 2b in THF FeCl 3 in THF BH 3 THF in THF for CSTR 2 BH 3 THF in THF for CSTR 6 Total The same reactor block set-up was used except tetraglyme solutions of NaBH 4 were replaced with solutions of BH 3 THF in THF. S9

10 Procedure Once all the solutions were prepared they were connected to the appropriate tubing as shown in Figure S2 and Figure S3 and placed under a nitrogen atmosphere. The reactor block was maintained at 20 C via circulation of silicon oil from a Julabo heating unit. The four lines were primed with suspension/solutions and then the suspension of 2b (20 g, mmol, in 73 ml THF) and FeCl 3 solution (13.15 g, mmol, 1 eq., in 68 ml THF) are simultaneously pumped into CSTR 1. Once this mixture begins to enter CSTR 2 the main solution of BH 3 THF in THF (81.1 ml of 1 M solution, 81.1 mmol, 1 eq.) was pumped into the reaction block at which point hydrogen gas evolution begins and the suspension becomes an yellow/green solution. When this solution starts to enter CSTR 6 the second solution of BH 3 THF in THF (16.2 ml of 1 M solution, 16.2 mmol, 0.2 eq.) was pumped into the reaction block. The reaction mixture was transferred from the top of the reaction block into a flask containing aqueous citric acid (7.79 g, mmol, 0.5 eq., in 60 ml water). The hydrogen gas accumulated in this flask is safely diluted with nitrogen gas (below 4 vol. % H 2 in the mixture as per ISO standard) and was released into the atmosphere. When all suspension 2b was added into the reactor block the flask was rinsed with 10 ml THF and pumped into the reactor to quantify the transfer of 2b. At this point all the reagent flasks were changed to flasks containing THF and continue to pump at their original flow rates for an additional 5 minutes while collecting reaction mixture in the receiving flask. This aqueous phase was separated and discarded and the organic phase was concentrated to 150 ml. The solution was diluted with n-buoh (20 ml), water (40 ml) and the phases were separated. The organic phase was washed twice with water (40 ml) then concentrated to 40 ml. The solution was diluted with n-buoh (40 ml) and concentrated to 40 ml. The organic phase was diluted once more with n-buoh (60 ml) and concentrated to 40 ml at which time some solids precipitate. The suspension was charged with 34-37% aqueous HCl (8.19 g, mmol, 1 eq.), heated to 65 C for 3 hours then slowly cooled to C and maintained at that temperature for hours. The suspension was filtered at C, washed with 10 ml cold (-10 to -5 C) n-buoh then dried under vacuum to provide g (66.5%) of 3b with an HPLC purity of a% (Figure S5) (impurity 5 retention time of minutes). Proton NMR data of 3b: 1 H-NMR (DMSO-d6): δ (ppm) 11.41(br s, 1H), 8.09 (s, 1H), 7.52 (d, 1H, J = 8.4 Hz), 7.42 (dd, 1H, J = 1.5 Hz and J = 8.4 Hz), 7.35 (d, 1H, J = 1.7 Hz), 3.68 (m, 2H), 2.75 (m, 2H), 1.77 (m, 4H). S10

11 Figure S5: HPLC chromatogram of 3b obtained after BH 3 THF reduction of 2b in ACR P200 S11

12 BH3 THF reductive deoxygenation of 2b in three jacketed CSTRs A diagram of the three jacketed CSTR set-up is provided in Figure S5 with a picture of the setup in Figure S6 and a close-up of the magnetic mixer in Figure S7. Preparation of a suspension of 2b in THF: A 100 ml round bottomed flask was charged with 2b (30 g, mmol) and THF (105 ml) and stirred at C gently to avoid splatter on the flask walls. Total suspension volume was 135 ml. Preparation of FeCl 3 solution in THF: A100 ml 2 necked round bottomed flask was charged with THF (103 ml), the headspace was purged with nitrogen gas and FeCl 3 (19.73 g, mmol, 1 eq.) was added slowly through a solids addition apparatus under nitrogen gas. The addition is exothermic and the rate was adjusted to maintain a solution temperature of <30 C. This solution was then transferred via cannula to a conical flask. Total volume of the green solution was 105 ml. BH 3 THF was purchased from Sigma-Aldrich as a 1 M solution in THF (item # ML) and used as is. One equivalent ( mmol, ml) of BH 3 THF was charged into the reactor from CSTR 2 and 0.2 eq. (24.32 mmol, 24.3 ml) was charged from CSTR 6. Total reaction volume: CSTR 1 and CSTR 2 reaction volumes were 20 ml and CSTR 3 reaction volume was 30 ml with a total reaction volume of 70 ml used to calculate the total flow rate of 14 ml/min for a 5 minute residence time. The volume in each CSTR was controlled by turning the subsequent pump on when the CSTR was filled to its desired volume. Table S3: Solution/slurry flow rates: Solution Total volume (ml) Flow rate (ml/minute) 2b in THF FeCl 3 in THF BH 3 THF in THF BH 3 THF in THF for CSTR Total Procedure: Once all the solutions were prepared they were connected to the appropriate tubing as shown in Figure S6 and Figure S7 and placed under a nitrogen atmosphere. The magnetic mixer was maintained at 20 C by a water bath and the three CSTRs were maintained at 20 C by circulation through the jacketed reactors. The three lines and the syringe needle were primed with suspension/solution and then the suspension of 2b (30 g, mmol) in THF (105 ml) and solution of FeCl 3 (19.73 g, mmol, 1 eq.) in THF (103 ml) were added together at the S12

13 first tee (See Figure S8). Once this mixture reached the second tee the addition of BH 3 THF ( mmol, ml, 1 M) solution in THF was started. The mixture is passed through a magnetic mixer which is cooled to maintain an exit temperature of 20 C (monitored by a thermocouple). The reaction mixture then passes through three CSTRs before being transferred to the collection flask and quenched with an aqueous citric acid solution. Each CSTR is connected to nitrogen line so that the hydrogen gas generated is safely diluted with nitrogen gas (below 4 vol. % H 2 in the mixture as per ISO standard) and released into the atmosphere. Each flask is marked with a specific volume, when this volume (20 or 30 ml) is reached a pump is started to begin transfer to the next CSTR. The working volume of each CSTR along with the flow rates of the different reagents accounts for the residence time of the reaction. When all suspension 2b was added into the CSTRs the flask was rinsed with 10 ml THF and pumped into the reactor to quantify the transfer of 2b. At this point all the reagent flasks were change to flasks containing THF and continued to pump at their original flow rates for an additional 5 minutes while collecting reaction mixture in the collection flask. This aqueous phase was separated and discarded and the organic phase was concentrated to 300 ml. The solution was diluted with n- BuOH (60 ml), water (60 ml) and the phases were separated. The organic phase was washed twice with water (60 ml) then concentrated to 60 ml at which point a suspension formed. The suspension was heated to 65 C, charged with 34-37% aqueous HCl (12.45 g, mmol, 1 eq.), maintained at 65 C for 3 hours then slowly cooled to C and maintained at that temperature for hours. The suspension was filtered at C, washed with 15 ml cold (-10 to -5 C) n-buoh then dried under vacuum to provide g (71%) of 3b with an HPLC purity of a% (Figure S9) (impurity 5 retention time of min). Proton NMR data of 3b: 1 H-NMR (DMSO-d6): δ (ppm) 11.41(br s, 1H), 8.09 (s, 1H), 7.52 (d, 1H, J = 8.4 Hz), 7.42 (dd, 1H, J = 1.5 Hz and J = 8.4 Hz), 7.35 (d, 1H, J = 1.7 Hz), 3.68 (m, 2H), 2.75 (m, 2H), 1.77 (m, 4H). Table S4 shows the reaction progression between the three different CSTRs. Most of the conversion occurs in CSTR 1 but the two other CSTRs are required to completely consume 2b and reduce the amount of intermediate 4. The rate of hydrogen gas generated during reaction was 98.9 ml/min. Before releasing to atmosphere, hydrogen gas was diluted with nitrogen gas (below 4 vol. % H 2 in a mixture, as per ISO standard) and was released in the atmosphere. S13

14 Figure S6: Schematic drawing of three jacketed CSTR set-up Figure S7: Picture of three jacketed CSTR set-up S14

15 Figure S8: Closer look at the magnetic mixer set-up Table S4: HPLC data of the three CSTR contents at steady state HPLC a% 2b Intermediate 4 3b Impurity 5 CSTR CSTR CSTR S15

16 Figure S9: HPLC chromatogram of 3b obtained after BH 3 THF reduction of 2b in three jacketed CSTRs S16

17 LCMS Sample: During our early experiments on the ACR P200 where a solution of 1.1 equivalents of NaBH 4 in diglyme was used a sample from the outlet was taken half way through the entire experiment, quenched with 2 drops of aq. citric acid and submit for HPLC. This same sample was then used for LC/MS to obtain the exact mass of intermediate 4. m/z ion Formula Abundance (M+H)+ C13H12ClN Difference Abs Diff Formula (M) Ion Formula Score Mass Calc. mass DBE (ppm) (ppm) C13H11ClN2 C13H12ClN NC Cl N 7 C 13 H 11 ClN 2 molecular weight = g/mol exact mass = amu Calculated exact mass = amu Obtained exact mass = amu Figure S10: LC/MS data for intermediate 4 S17