Mild Decarboxylative Activation of Malonic Acid Derivatives by 1,1 - Carbonyldiimidazole. Danny Lafrance*, Paul Bowles, Kyle Leeman and Robert Rafka

Transcription

1 Mild Decarboxylative Activation of Malonic Acid Derivatives by 1,1 - Carbonyldiimidazole. Danny Lafrance*, Paul Bowles, Kyle Leeman and Robert Rafka Development Science and Technology, Pfizer Inc., Eastern Point Road, Groton, Connecticut Danny.lafrance@pfizer.com Index: General information...s1 Experimental procedure for C 2 volume calculation S2 Experimental procedure for solvent screen study..s2 Synthesis and characterization of compound 1a...S2 General procedure and characterization of compound 1b-7b, 10b...S3 Synthesis and characterization of compound 1c S6 Synthesis and characterization of compound 1d...S6 Synthesis and characterization of compound 1e S7 Synthesis and characterization of compound 1f S7 Synthesis and characterization of compound 1g...S8 References..S9 MR spectra S10 IR spectra.s25 General information: Common substrates and reagents were obtained from commercial suppliers and used without further purification. All reactions were set-up in air and carried under an atmosphere of dry nitrogen. Dimethyl ketene was prepared according to a literature S1

2 procedure 1 and used directly for IR monitoring after zinc metal filtration through a 45 micron PTFE filter. GCMS data were collected on a Hewlett Packard HP 6890 Series GC system equipped with an Agilent 5973 detector. MR data were collected on a Bruker Ultrashield TM 400 plus instrument. HRMS data were collected on a Thermo-Fisher LTQ- rbitrap spectrometer. IR monitoring was performed using a Thermo icolet exus-470 FTIR instrument. Melting point were recorded using a Thomas Hoover Unimelt apparatus. For known compounds, the 1 H-MR, 13 C-MR and HRMS data are provided and were compared with literature reports. For new compounds or those with limited literature data available (3b, 10b, 1d 1e, 1g), full characterization is included. Experimental procedure for C 2 volume calculation A 3 neck 50 ml round bottom flask was equipped with a magnetic stirrer, capped with rubber septa and connected at one outlet with a piece of flexible Tygon TM tubing. The tubing was inserted into an inverted 100 ml graduated cylinder filled with water and held in place in a water bath at 19.3 C. The reaction flask was then added 15 ml of THF, 1g (6.24 mmols, 1 eq.) of diethylmalonic acid and 1.11g (6.86 mmols, 1.1 eq.) of 1,1 - Carbonyldiimidazole in one portion (quickly), after which the system is capped and the C 2 produced is allowed to fill the graduated cylinder. The gas production and displaced water volume stabilized after 90 minutes, to show a total volume of 146 ml. (calc = 150 ml for 2 moles of gas produced). Experimental procedure for solvent screen study In separate reaction tubes equipped with stir bars, charge 3.5 ml of the appropriate solvent (THF, DCM, Acetonitrile, Toluene, Ethyl Acetate and DMF). To each tube is added 250 mg of diethylmalonic acid (1.56 mmols, 1.0 eq.) and 266 mg of 1,1 - Carbonyldiimidazole (1.64 mmols, 1.05 eq.) in one portion. Stir the reaction mixture at room temperature (22 C) and take a 50 microliter aliquot with a micro-syringue. Dilute in a 1 ml volume of acetonitrile, filter the solution over 45 micron PTFE filter and analyse the filtrate by GCMS. The chromatograms are very clean and the conversion is measured by comparing product with residual malonic acid starting material. Results are: THF (95%), DCM (92%), Acetonitrile (96%), Toluene (71%), Ethyl Acetate (95%), DMF (88%). Synthesis and characterization of compound 1a In a 50 ml round bottom flask, charge 10 ml of THF, 1g (6.24 mmols, 1.0 eq.) of diethylmalonic acid and add 1.11g (6.85 mmols, 1.1 eq.) of 1,1 -Carbonyldiimidazole S2

3 portionwise (gas evolution) under a positive dry nitrogen flow. Stir at room temperature for 1 hr and add a 20 ml water solution of citric acid monohydrate (1.31g, 1.0 eq.). The aqueous phase is then extracted with 20 ml of diethyl ether. The organic phase is washed with brine, dried over magnesium sulfate, filtered and concentrated in vacuo to give 0.83g (80%) of a light yellow oil. Compound 1a was previously reported 2 but it was generated in-situ and reacted right away due to its limited shelf live. Here we were able to isolate a pure sample and obtain MR data (the sample was later found to degrade to a dark color when left on the bench at room temperature overnight). 1 H MR (400 MHz, CDCl 3 ) δ: 8.18 (s, 1H), 7.49 (s, 1H), 7.07 (s, 1H), 2.86 (m, 1H), (m, 2H), (m, 2H), 0.9 (t, J = 8 Hz, 6H) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 172.9, 136.1, 130.9, 116.1, 48.2, 25.0, 11.5 ppm. General procedure and characterization of compound 1b-7b (all reaction run on a 1g scale of starting malonic acid) H 1b In a 50 ml round bottom flask, charge 15 ml of THF, 1g (6.24 mmols, 1.0 eq., limiting reagent in all reactions) of diethylmalonic acid and add 1.11g (6.85 mmols, 1.1 eq.) of 1,1 -Carbonyldiimidazole portionwise (gas evolution) under a positive dry nitrogen flow. Stir at room temperature with stirring for 1 hr. Add 1.02 ml ( 9.36 mmols, 1.5 eq.) of benzyl amine in one portion and stir at reflux (67 C) for 30 minutes. Allow the reaction mix to cool down to room temperature and remove the excess THF by concentrating in vacuo. The obtained residue is dissolved in 20 ml of ethyl acetate and the organic phase is successively washed with a 15 ml aqueous solution of citric acid monohydrate (1.31g, 6.24 mmols, 1.0 eq) and 10 ml of a saturated aqueous sodium bicarbonate solution. Dry the organic phase over sodium sulfate, filter and concentrate in vacuo. Get 1.15g (90%) of white solid. 1 H MR (400 MHz, CDCl 3 ) δ: (m, 5H), 6.04 (br s, 1H), 4.35 (d, J = 8 Hz, 2H), 1.82 (m, 1H), (m, 2H), (m, 2H), 0.81 (t, J = 8 Hz, 3H) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 175.8, 138.7, 128.6, 127.8, 127.4, 51.4, 43.4, 25.8, 12.2 ppm. HRMS (ES, 2 ) calcd for C 13 H , found MR data match those previously reported. 3 S3

4 Same conditions as 1b. Get 1.31g (98%) of a thick oil that crystallize upon standing. 1 H MR (400 MHz, CDCl 3 ) δ: (m, 5H), 6.66 (br s, 1H), 4.26 (d, J = 8 Hz, 2H), 2.06 (t, J = 8 Hz, 2H), (m, 2H), 0.82 (t, J = 8 Hz, 3H) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 173.4, 138.6, 128.6, 127.6, 127.3, 43.4, 38.5, 19.2, 13.8 ppm. HRMS (ES, 2 ) calcd for C 11 H , found MR data match those previously reported. 4 Same conditions as 1b. Get 1.22g (100%) of oil that slowly crystallize upon standing. MP = C (lit C). 5 1 H MR (400 MHz, CDCl 3 ) δ: (m, 8H), 7.02 (d, J = 8 Hz, 2H), 6.05 (br s, 1H), 4.30 (dd, J = 12, 4 Hz, 1H), 4.17 (dd, J = 12, 4 hz, 1H), 3.18 (t, J = 8 Hz, 1H), 2.09 (m, 1H), 1.7 (m, 1H), 0.78 (t, J = 8 Hz, 3H) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 173.7, 140.0, 138.4, 128.8, 128.6, 128.0, 127.5, 127.3, 127.2, 55.1, 43.5, 26.4, 12.4 ppm. IR (neat): 3284, 3065, 2830, 1636, 1495, 1226, 1041, 731, 664; HRMS (ES, 2 ) calcd for C 17 H , found Same conditions as 1b. Get 1.15g (92%) of white solid. 1 H MR (400 MHz, CDCl 3 ) δ: (m, 8H), 7.08 (d, J = 8 Hz, 2H), 5.9 (br s, 1H), 4.30 (d, J = 4 Hz, 2H), 3.5 (s, 2H) ppm. 13 C MR 400 MHz, CDCl 3 ) δ: 171.0, 138.2, 134.9, 129.5, 129.0, 128.7, 127.5, 127.4, 127.3, 43.8, 43.6 ppm. HRMS (ES, 2 ) calcd for C 15 H , found MR data match those previously reported. 6 Same conditions as 1b. Get 1.05g (83%) of white solid. 1 H MR (400 MHz, CDCl 3 ) δ: (m, 5H), 5.81 (br s, 1H), 4.34 (d, J = 4 Hz, 2H), (m, 1H), 1.8 (d, J = 12 Hz, 2H), 1.71 (dd, J = 12, 2 Hz, 2H), (m, 1H), 1.39 (qd, J = 12, 2 Hz, 2H), (m, 3H) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 176.0, 138.6, 128.7, 127.7, 127.4, S4

5 45.6, 43.4, 29.7, 25.7, 25.7 (overlap) ppm. HRMS (ES, 2 ) calcd for C 14 H , found MR data match those previously reported. 7 Same conditions as 1b. Get 1.1g (85%) of white powder. 1 H MR (400 MHz, CDCl 3 ) δ: (m, 5H), 5.92 (br s, 1H), 4.34 (d, J = 4 Hz, 2H), 2.46 (p, J = 8 Hz, 1H), (m, 6H), (m, 2H) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 176.2, 138.7, 128.7, 127.7, 127.4, 45.8, 43.5, 30.5, 26.0 ppm. HRMS (ES, 2 ) calcd for C 13 H , found MR data match those previously reported. 8 Same conditions as 1b. Get 1.17g (89%) of white powder. 1 H MR (400 MHz, CDCl 3 ) δ: (m, 5H), 6.17 (br s, 1H), 4.28 (d, J = 4Hz, 2H), 2.94 (p, J = 8 Hz, 1H), (m, 2H), (m, 2H), (m, 2H) ppm. 13 C MR 400 MHz, CDCl 3 ) δ: 175.0, 138.6, 128.6, 127.7, 127.3, 43.4, 39.8, 25.4, 18.2 ppm. HRMS (ES, 2 ) calcd for C 12 H , found nly 1 H-MR data has been reported. 9 Same conditions as 1b. The crude isolated solid consisted in a mixture of the desired product and, -Dibenzylurea side product. The pure product was obtained by separation using a slurry packed Merck flash silica column and eluting with 7/1/0.1 v/v/v Toluene/Acetone/MeH solution. Get 0.26g (19%) of white powder. MP = C. 1 H MR (400 MHz, CDCl 3 ) δ: (m, 5H), 6.7 (br s, 1H), 4.87 (d, 2 J H-F = 48 Hz, 2H), 4.55 (d, 5 J H-F = 4 Hz, 2H) ppm. 19 F-MR (377 MHz, CDCl 3 ) δ: (t, 2 J H-F = 48 Hz) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: (d, 2 J C-F = 20 Hz), 137.4, 128.9, 127.9, 127.8, (d, 1 J C-F = 185 Hz), 42.9 ppm. HRMS (ES, 2 ) calcd for C 9 H 10 F , found S5

6 Synthesis and characterization of compound 1c H 1c In a 25 ml flask equipped with a stir bar, charge 10 ml THF, 1g (6.24 mmols, 1.0 eq.) of diethylmalonic acid and 1.11g (6.85 mmols, 1.1 eq) of 1,1 -Carbonyldiimidazole portionwise (off-gasing) and stir the reaction mixture at room temperature for 1 hr. Add a 2 ml aqueous solution of 374 mg (9.35 mmols, 1.5 eq.) of sodium hydroxide in one portion and stir the reaction mixture for 1 hr at room temperature. Concentrate in vacuo to a residue and take in 25 ml of 1 HCl (25 mmols, 4 eq.). Verify that ph 1. Extract the aqueous phase 2 times with 10 ml DCM, combine organics, dry over sodium sulfate and concentrate in vacuo. Get 0.66g (90%) of clear oil. 1 H MR (400 MHz, CDCl 3 ) δ: 11.7 (br s, 1H), 2.16 (m, 1H), (m, 4H), 0.87 (t, J = 8 Hz) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 183.1, 48.7, 24.7, 11.7 ppm. MR data match those obtained from commercially available 2-Ethylbutyric acid. In a 65 ml flask equipped with a stir bar, charge 15 ml of THF, 1g (6.24 mmols, 1.0 eq.) of diethylmalonic acid and 1.11g (6.85 mmols, 1.1 eq) of 1,1 -Carbonyldiimidazole portionwise (off-gasing) and stir the reaction mixture at room temperature for 1 hr. Add 2.06g (17.8 mmols, 2.85 eq.) of sodium tert-amylate as a solid portionwise, followed by 76 mg (0.62 mmols, 0.1 eq) of DMAP, and stir the reaction mixture at room temperature for 3hr. Dilute with 15 ml of water and extract the aqueous phase twice with 10 ml of diethyl ether. Combine the ether phase and wash sequentially with a 10 ml aqueous solution of 1.31g (6.24 mmols, 1 eq.) of citric acid monohydrate, followed by 10 ml of saturated sodium bicarbonate and 10 ml brine. The organic solution is then dried over sodium sulfate and concentrated in vacuo. Get 1.05g (91%) of clear oil. 1 H MR (400 MHz, CDCl 3 ) δ: 2.01 (m, 1H), 1.69 (q, J = 8Hz, 2H), (m, 4H), 1.35 (s, 6H), 0.83 (t, J = 8 Hz, 9H) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 175.6, 82.2, 50.0, 33.8, 25.5, 25.3, 11.8, 8.2 ppm. IR (neat): 2966, 2935, 2878, 1726, 1460, 1384, 1270, 1144, 943, 630; HRMS: Poor ionization. Fragmentation pattern from GC is consistent with the product: GC (m/z) M calc. for C 11 H 22 2 : Found: 71 (100%), M C 6 H 11 2 ; 99 (35%), M C 5 H 11 ; 142 (<5%), M C 3 H 8 ; 157 (<5%), M C 2 H 5 ; 171 (<5%), M CH 3 ; 187 (<5%), M + H. S6

7 In a 50 ml flask equipped with a stir bar, charge 20 ml of THF, 1g (6.24 mmols, 1.0 eq.) of diethylmalonic acid and 1.11g (6.85 mmols, 1.1 eq) of 1,1 -Carbonyldiimidazole portionwise (off-gasing) and stir the reaction mixture at room temperature for 1 hr. Add 0.92g (9.43 mmols, 1.5 eq.) of,-dimethylhydroxylamine hydrochloride followed by 2.59g (18.7 mmols, 3 eq.) of potassium carbonate and 76 mg (0.62 mmols, 0.1 eq.) of DMAP. Stir the reaction mixture at reflux until complation (96% conversion after 7hr by GCMS). Allow the reaction mix to cool down to room temperature, filter over a pad of celite and wash solids with THF. The filtrate is concentrated in vacuo and the residue is added 15 ml of water and 15 ml of ethyl acetate. Split aqueous and wash the organic phase sequentially with a 10 ml aqueous solution of 1.31g (6.24 mmols, 1 eq.) of citric acid monohydrate, followed by 10 ml of saturated sodium bicarbonate and 10 ml brine. The organic solution is then dried over sodium sulfate and concentrated in vacuo. Get 0.84g (85%) of colorless oil. 1 H MR (400 MHz, CDCl 3 ) δ: 3.62 (s, 3H), 3.14 (s, 3H), 2.64 (br s, 1H), (m, 2H), (m, 2H), 0.81 (t, J = 8Hz) ppm. 13 C MR (100 MHz, CDCl 3 ) δ: 178 (weak), 61.4, 43.9, 32.0, 25.4, 12.1 ppm. IR (neat): 2964, 2935, 2876, 1658, 1461, 1388, 1177, 998, 733; HRMS (ES, 2 ) calcd for C 8 H , found In a 50 ml flask equipped whit a stir bar, charge 10 ml THF, 1g (6.24 mmols, 1.0 eq.) of diethylmalonic acid and 1.11g (6.85 mmols, 1.1 eq) of 1,1 -Carbonyldiimidazole portionwise (off-gasing) and stir the reaction mixture at room temperature for 1 hr. Add 1.1g (6.42 mmols, 1.03 eq.) of 4-Methyl-benzenesulfonamide in one portion, 76 mg (0.62 mmols, 0.1 eq.) of DMAP, followed by the dropwise addition of a 3 ml THF solution of 1 ml (6.65 mmols, 1.07 eq.) of DBU. After the base addition is complete, stir at room temperature for 18 hr (overnight). The crude reaction mixture is poured into 30 ml of 1 HCl and the resulting mixture is concentrated in-vacuo to remove excess THF. The aqueous phase is extracted with 20 ml of ethyl acetate, and the organic phase is washed with 10 ml of brine, dried over sodium sulfate and concentrated in vacuo. The residue is purified by flash chromatography over silica gel using DCM/MeH(1 to 4%) as the eluant. The product containing fractions are pooled and concentrated in vacuo to yield 1.33g (79%) of a thick, colorless oil that crystallizes upon standing. 1 H MR (400 MHz, CDCl 3 ) δ: 9.35 (br s, 1H), 7.96 (d, J = 8 Hz, 2H), 7.34 (d, J = 8 Hz, 2H), 2.44 (s, 3H), 2.08 (m, 1H), (m, 4H), 0.76 (t, J = 8Hz, 6H) ppm. 13 C MR (100 MHz, S7

8 CDCl 3 ) δ: 174.5, 145.1, 135.6, 129.6, 128.3, 50.6, 25.0, 21.7, 11.5 ppm. MR data match those previously reported. 10 In a 50 ml flask (A) equipped with a stir bar, charge 20 ml acetonitrile, 2.23g (13.1 mmols, 2.1 eq) of ethyl potassium malonate, 2.7 ml (19.4 mmols, 3.1 eq.) of triethylamine and 1.49g (15.7 mmols, 2.5 eq.) of magnesium dichloride. Stir at room temperature for 2 hr. In a separate 25 ml flask (B), charge 10 ml THF, 1g (6.24 mmols, 1.0 eq.) of diethylmalonic acid and 1.11g (6.85 mmols, 1.1 eq) of 1,1 -Carbonyldiimidazole portionwise (off-gasing) and stir the reaction mixture at room temperature for 1 hr. nce the reaction in flask A is completed (2hr), add the content of flask B to flask A in one portion and stir the reaction mixture at room temperature for 18 hr (overnight), and complete the reaction by stirring at reflux for an additional 2hr. After the reaction was allowed to cool down, 20 ml of 13% HCl aqueous solution was carefully added, keeping T 25 C, and the resulting mixture was stirred at room temperature for 15 minutes. Allow phases to separate and discard aqueous phase. Concentrate the organic phase in vacuo and take the residue in 20 ml of water. Extract aqueous with 20 ml of ethyl acetate, discard aqueous phase and wash the organics sequentially with 10 ml of saturated sodium bicarbonate solution, 10 ml of brine, dry over sodium sulfate and concentrate in vacuo. Get 0.78g (67%) of light, pale yellow oil. 1 H MR (400 MHz, CDCl 3 ) δ: 4.12 (q, J = 8Hz, 2H), 3.38 (s, 2H), 2.39 (m, 1H), (m, 2H), (m, 2H), 1.2 (t, J = 8 Hz, 3H), 0.81 (t, J = 8 Hz, 6H) ppm. Both the 1 H-MR and 13 C-MR are consistent with a mixture of tautomers. The 13 C- MR show the 2 distinctive products with all peaks fully separated, and each tautomeric form from the same spectra is presented below in a separated format: 1g 13 C MR (100 MHz, CDCl 3 ) δ: 206.3, 167.2, 61.2, 55.4, 48.5, 23.6, 14.1, 11.5 ppm. 1g* 13 C MR (100 MHz, CDCl 3 ) δ: 181.1, 172.7, 89.74, 59.8, 49.2, 25.4, 21.0, 11.8 ppm. IR (neat): 2967, 2878, 1747, 1712, 1644, 1307, 1232, 632; HRMS (ES, 2 ) calcd for C 10 H , found S8

9 References. (1) Baigrie, L.M.; Lenoir, D. J. rg. Chem. 1985, 50, (2) Rannard, S.P.; Davis,.J. rg. lett. 2000, 2, 2. (3) Tosikatsu, M.; Kazuaki, I. rg. Lett. 2006, 8, (4) Allen, C.L.; Davulcu, S. rg. Lett. 2010, 12, (5) Skinner, G.S.; Perkins, J.S. J. Am. Chem. Soc. 1950, 72, (6) Ignatenko, V.A.; ihal, V.R. rg. Lett. 2010, 12, (7) Maki, T.; Ishihara, K. rg. Lett. 2006, 8, (8) Sudrik, S.G.; Chavan, S.P. J. rg. Chem. 2002, 67, (9) Although the 1 H-MR data generally match the one reported, it appears to have been run with a low resolution instrument, making an exact match of structure difficult: h, S.J.; Jung, K.H. Bull. Kor. Chem. Soc. 2007, 28, (10) Baumann, T.; baechle, M. rg. Lett. 2006, 8, S9

10 1a S10

11 H 1b S11

12 H 2b S12

13 3b H S13

14 H 4b S14

15 H 5b S15

16 H 6b S16

17 H 7b S17

18 F H 10b S18

19 F H 10b ( 19 F-MR) S19

20 H 1c S20

21 1d S21

22 1e S22

23 S H 1f S23

24 S benzyl-2-phenylbutanamide %Transmittance Wavenumbers (cm-1) 1g

25 S benzyl-2-phenylbutanamide %Transmittance Wavenumbers (cm-1) H 3b

26 1d 110 tert-pentyl-2-ethylbutanoate %Transmittance Wavenumbers (cm-1) S26

27 S ethyl--methoxy--methylbutanamide %Transmittance Wavenumbers (cm-1) 1e

28 1g 110 ethyl-4-ethyl-3-oxohexanoate %Transmittance Wavenumbers (cm-1) S28