Preparation of 1-Benzyl-7-methylene-1,5,6,7-tetrahydro-

4H-benzo[d]imidazol-4-one
Michael Morgen, Jasmin Lohbeck, and Aubry K. Miller1*
Cancer Drug Development Group, German Cancer Research Center (DKFZ),
69126 Heidelberg, Germany

Checked by Nageswara Rao Kalikinidi, Venumadhav Janganati, Gopal Sirasani,

and Chris Senanayake

Procedure (Note 1)

A. 1-(1-Benzyl-5-iodo-1H-imidazol-4-yl)pent-4-en-1-one (2). A 250 mL

round-bottomed flask equipped with a 3.2 cm long oval stir bar is charged
with 1-(5-iodo-1H-imidazol-4-yl)pent-4-en-1-one (1) (14.00 g, 50.71 mmol,
1.0 equiv) (Note 2) followed by DMF (100 mL) (Note 3). The flask is capped
with a rubber septum and the resulting, orange-colored solution is
magnetically stirred (500 rpm) and cooled to 0 °C using an ice bath.
Potassium carbonate (10.51 g, 76.06 mmol, 1.5 equiv) (Note 4) is added in one
portion followed by the addition of benzyl bromide (6.3 mL, 53.2 mmol,

Org. Synth. 2021, 98, 315-342 315 Published on the Web 9/20/2021
DOI: 10.15227/orgsyn.098.0315 Ó 2021 Organic Syntheses, Inc.
1.05 equiv) (Note 5) dropwise using a syringe over a time period of 2 min.
The resulting suspension is stirred at 0 °C for 2 h (Figure 1A). Analysis by
TLC (Note 6) is performed to ensure that starting material is consumed. After
1 is entirely consumed the reaction mixture is transferred to a 1 L separatory
funnel. The reaction vessel is sequentially rinsed with H2O (50 mL) (Note 7)
and EtOAc (50 mL) (Note 8), both of which are transferred to the separatory
funnel. Additional H2O (250 mL) and EtOAc (250 mL) are added to the
separatory funnel. After mixing, the phases are separated, and the aqueous
phase is extracted with EtOAc (2 x 200 mL) (Figure 1B). The combined
organic phases are sequentially washed with water (2 x 300 mL) and a
saturated aqueous NaCl solution (300 mL). The organic layer is dried with
MgSO4 (40 g) (Note 9), filtered through a fluted filter paper into a 1 L round-
bottomed flask using a glass funnel (Note 10), and concentrated on a rotary
evaporator (40 °C, 180 to 15 mmHg) (Note 11). The product is purified by
crystallization by dissolving the solid in a minimal amount of EtOAc
(100 mL) (Notes 12 and 13) on a gently boiling water bath. To the boiling hot
solution is added, in portions, n-hexane (80 mL) (Note 14) to the point where
the white precipitate that forms upon addition slowly disappears. The flask
is then covered with a plastic cap, sealed with Parafilm, and the solution is
allowed to cool to 24 °C on the bench and then at 4 °C in a refrigerator for
18 h (Figure 1C). The obtained solid is vacuum filtered through a round filter
paper (ø = 9 cm) using a Büchner funnel and washed with a minimum
amount of cold (4 °C) EtOAc/n-hexane 1:1 (approx. 20 mL) and then cold
(4 °C) n-hexane (2 x 20 mL) (Note 15). The mother liquor is concentrated on a
rotary evaporator (40 °C, 280 to 15 mmHg) and the remaining residue is
crystallized as described above using a smaller solvent volume to obtain a
second crop of material. The combined solids are dried under high vacuum
(24 °C, 2 x 10-2 mm Hg) at 24 °C for 18 h to give 13.0 g (35.5 mmol, 70%) of 2
as an off-white solid (Notes 16, 17, and 18) (Figure 1D).

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Figure 1. (A) Reaction mixture after addition of benzyl bromide; (B) Phases
(EtOAc, top; aqueous, bottom) after shaking and allowing to separate; (C)
Crystallization of 2 from a mixture of EtOAc and n-hexane; (D) Final
product 2 dried under high vacuum (photos provided by submitters)

B. 1-Benzyl-7-methylene-1,5,6,7-tetrahydro-4H-benzo[d]imidazol-4-one (3). A
500 mL beaker (ø = 7 cm, h = 9 cm) (Note 19) equipped with a triangular
prism-shaped stir bar (50 x 12 mm) is charged with tetra-n-butylammonium
bromide (52.82 g, 163.84 mmol, 5.0 equiv) (Note 20) and tetra-n-
butylammonium acetate (24.70 g, 81.92 mmol, 2.5 equiv) (Note 21). The flask
is submerged in an oil bath preheated to 130 °C (Figure 2A). The salts are
magnetically stirred (270 rpm) until a pale-yellow, homogenous melt is
obtained (approximately 30 min) (Figure 2B) (Note 22). Then Pd(OAc)2
(220.7 mg, 0.98 mmol, 0.03 equiv) (Note 23) is added in one portion to the
melt (Note 24). The mixture is stirred for 1 min (Note 25), whereupon 1-(1-
benzyl-5-iodo-1H-imidazol-4-yl)pent-4-en-1-one (2) (12.00 g, 32.77 mmol,
1.0 equiv) is added slowly but continuously in one portion to the melt (Notes
24 and 26).
The resulting dark brown melt (Figure 2C) is magnetically stirred
(270 rpm) for 5–10 min, at which time TLC monitoring shows complete
consumption of the starting material (Note 27). The reaction is stopped by
pouring the hot melt into a 1 L Erlenmeyer flask that contains a mixture of
EtOAc and water (300 mL each) and is equipped with a 5 cm long stir bar that
is magnetically stirred (500 rpm) at 24 °C (Note 28) (Figure 2D). Complete

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transfer is assured by repeatedly rinsing the reaction vessel with EtOAc and
H2O from a squirt bottle. The phases are vigorously stirred for 5 min and then
filtered through a firmly packed pad (2 cm) of Celite (Note 29) in a sintered
glass Büchner funnel (ø = 10 cm, h = 15 cm; Porosity 4). (Figure 2E).

Figure 2: (A) The mixture of (n-Bu)4NOAc and (n-Bu)4NBr immediately

after being immersed in the oil bath; (B) Appearance of the two salts after
they have completely melted; (C) Appearance of the melt after adding
Pd(OAc)2 and 2; (D) Hot melt being poured into a stirring mixture of EtOAc
and H2O at 24 °C; (E) Filtration of the two phases through a pad of Celite
using a sintered glass funnel (photos provided by submitters)

The Celite pad is washed with additional EtOAc (400 mL), and the phases
are transferred into a 1 L separatory funnel and separated. The organic phase
is washed with H2O (6 x 200 mL) (Figure 3A) until TLC monitoring showed
no remaining tetrabutylammonium salts in the organic layer (Notes 30, 31
and 32). The organic phase is then washed with 1 M aqueous NaOH
(10 x 50 mL) (Figure 3B and 3C) (Note 33 and 34) followed by a final wash
with saturated aqueous NaCl solution (200 mL). The organic phase is
transferred into a 1 L round-bottomed flask equipped with a 3.2 cm long oval
stir bar and capped with a rubber septum. To this red solution is added
activated carbon (1.0 g) (Note 35). The mixture is stirred (500 rpm) at 24 °C
for 18 h and afterwards filtered through a firmly packed (2 cm) pad of Celite
(Figure 3D) (Note 36) in a sintered glass Büchner funnel (ø = 10 cm,
h = 15 cm; Porosity 4). This Celite pad is washed with EtOAc (400 mL) and
the obtained pale, yellow-colored solution is concentrated to roughly half its
volume on a rotary evaporator (40 °C, 120 mmHg). To this solution is added
n-hexane (400 mL), whereupon the product precipitates (Figure 3E)
(Note 37). The resultant suspension is concentrated on a rotary evaporator

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(40 °C, 225 to 15 mmHg) to dryness (Note 38). The yellow solid is transferred
into a sintered glass Büchner funnel (ø = 6 cm, h = 6 cm; Porosity 4)
(Figure 3F) (Note 39), thoroughly washed with n-hexane (500 mL) at 24 °C
(Note 40), and dried under high vacuum (24 °C, 2 x 10-2 mmHg) for 18 h.
Imidazole 3 (4.3 g, 18.1 mmol, 55%) is obtained as a tan-colored solid
(Figure 4) (Notes 18, 41 and 42). An aromatic by-product is also produced in
the reaction (Note 43).

Figure 3. (A) Washing of the organic phase with water; (B) Subsequent
washing of the organic phase with 1 M NaOH; (C) Appearance of the
aqueous phases (1 – 10) from basic washing procedure; (D) Filtration of the
organic phase through a pad of Celite after charcoal treatment; (E)
Suspension formed after half concentration of the organic phase and
addition of n-hexane; (F) Washing of 3 with n-hexane using a sintered glass
frit (photos provided by submitters)

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 Figure 4. Appearance of pure product 3 (photo provided by submitters)

Notes

1. Prior to performing each reaction, a thorough hazard analysis and risk

assessment should be carried out with regard to each chemical substance
and experimental operation on the scale planned and in the context of the
laboratory where the procedures will be carried out. Guidelines for
carrying out risk assessments and for analyzing the hazards associated
with chemicals can be found in references such as Chapter 4 of “Prudent
Practices in the Laboratory” (The National Academies Press,
Washington, D.C., 2011; the full text can be accessed free of charge at
https://www.nap.edu/catalog/12654/prudent-practices-in-the-
laboratory-handling-and-management-of-chemical. See also
“Identifying and Evaluating Hazards in Research Laboratories”
(American Chemical Society, 2015) which is available via the associated
website “Hazard Assessment in Research Laboratories” at
https://www.acs.org/content/acs/en/about/governance/committees
/chemicalsafety/hazard-assessment.html. In the case of this procedure,
the risk assessment should include (but not necessarily be limited to) an
evaluation of the potential hazards associated with dimethylformamide,
potassium carbonate, benzyl bromide, ethyl acetate, magnesium sulfate,
sodium chloride, hydrochloric acid, n-hexane, palladium(II) acetate,
tetra-n-butylammonium bromide, tetra-n-butylammonium acetate,
sodium hydroxide, benzene, methanol, and silica gel.
2. This compound was synthesized as previously described in Org. Synth.
2021, 98, 171–193.

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3. Dimethylformamide was obtained from Sigma Aldrich (≥99.8%) and was
used as received.
4. Potassium carbonate (anhydrous, ≥99%) was obtained from Sigma
Aldrich and was used as received.
5. Benzyl bromide (98.0%, reagent grade) was obtained from Sigma-Aldrich
and was used as received.
6. For reaction monitoring thin-layer chromatography was performed
using silica gel F254-plates from Merck, Darmstadt, Germany and a 1:1
mixture of EtOAc/n-hexane as eluent. A small sample (~50 L) was taken
from the reaction mixture with a glass pipette equipped with a silicone
bulb and quenched into H2O (~1 mL) and EtOAc (~0.2 mL) in an
Eppendorf tube. The two layers were agitated by pulling multiple times
into the pipette and then were allowed to separate in the tube. The
organic layer was used for TLC spotting. The starting material 1 shows
an Rf value of 0.2, whereas the desired product 2 shows an Rf value of
0.7 (both visible under UV light). If analysis does not indicate complete
consumption of 1, another portion of benzyl bromide (0.35 mL,
5.07 mmol, 0.1 equiv) is added, and the reaction is stirred at the same
temperature for an additional 1 h – the checkers found that addition of
this additional portion of benzyl bromide was necessary.

Figure 5. TLC monitoring of completed reaction using normal phase

silica plates and 1:1 EtOAc/n-hexane as eluent (left lane: starting
material; right lane: reaction mixture; middle lane: co-spot) (photo
provided by submitters)

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7. The submitters used deionized water from their in-house supply.
8. Ethyl acetate (≥99.8%) was obtained from Fisher Chemical and was used
as received.
9. Magnesium sulfate (97%, pure, anhydrous) was obtained from Acros
Organics and was used as received.
10. The remaining magnesium sulfate was washed with EtOAc (25 mL).
11. The crude product obtained by benzylation of imidazole 1 mainly
consists of 2 and its regioisomer 4 which are formed in a ratio of 6:1–8:1
(Figure 6).

Figure 6. Regioisomers obtained by benzylation of imidazole 2

The ratio can be determined by 1H NMR analysis of the crude product

mixture after extraction, but before crystallization (diagnostic signal
marked with red circle: desired product 2, 5.30 ppm; regioisomer 4,
5.50 ppm in DMSO-d6). The two regioisomers have very similar Rf values,
thus the desired (major) product is best purified by crystallization.
12. A wooden stick was placed in the flask to promote boiling and prevent
bumping.
13. In some cases, the volume of hot EtOAc (100 mL) could not dissolve all
of the solids. In these cases, the hot suspension was filtered through a
fluted filter paper into a 500 mL round-bottomed flask using a glass
funnel before continuing with the crystallization procedure. Analysis of
the filtered white solid by 1H NMR showed it to be the imidazolium salt 5
(Figure 7 and see discussion).

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 Figure 7. Poorly soluble imidazolium salt, which results from
dibenzylation

14. n-Hexane (≥95%, HPLC grade) was obtained from Fisher Chemical and
was used as received.
15. The solvent mixtures were cooled to 4 °C in a refrigerator prior to their
use for washing the final compound.
16. The solid was sometimes obtained as a powder, sometimes fine needles,
and sometimes thick plates (Figure 8). This variation appears to be
dependent on the rate of crystallization. NMR analysis revealed that all
forms are equally pure 2. The product 2 exhibits the following analytical
data: Rf = 0.70 (EtOAc/n-hexane 1:1). mp (uncorrected): 110–111 °C.
1
H NMR (600 MHz, DMSO-d6) δ: 2.27 – 2.38 (m, 2H), 3.02 (dd, J = 7.8,
7.0 Hz, 2H), 4.94 (d, J = 10.4 Hz, 1H), 5.03 (d, J = 17.1Hz, 1H), 5.30 (s, 2H),
5.85 (ddt, J = 17.2, 10.2, 6.4 Hz, 1H), 7.14-7.15 (m, 2H), 7.30 – 7.31 (m, 1H),
7.35 – 7.37 (m, 2H), 8.23 (s, 1H). 13C NMR (150 MHz, DMSO-d6) δ: 27.7,
37.3, 50.4, 80.6, 114.9, 127.1, 127.8, 128.7, 136.2, 137.9, 141.3, 141.4, 194.5.
LC-MS (M+H) calcd for C15H16N2OI (m/z): 367. HRMS–ESI (m/z)
(provided by submitters): [2M + Na]+ calcd for C30H30I2N4NaO2: 755.0350,
Found: 755.0357.

Figure 8. Appearance of 2 (left: needles; right: plates) from different

crystallizations (photos provided by submitters)

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17. Purity was determined to be 98.75% by qNMR spectroscopy in DMSO-d6
using 36 mg of compound (2) and 11.5 mg of mesitylene (96%) as an
internal standard.
18. The product showed no decomposition after storage at 24 °C on the
benchtop for one month.
19. The submitters suggest the use of a narrow beaker so that the melt has
reasonable depth and so that stirring of the melt results in a vortex that
facilitates the uptake and mixing of the added materials.
20. Tetra-n-butylammonium bromide (≥99.0%, reagent plus) was obtained
from Sigma-Aldrich and was used as received.
21. Tetra-n-butylammonium acetate (≥90%, technical) was obtained from
TCI Chemicals and was used as received.
22. The remaining salt residues sticking to the wall of the beaker were
brought into the melt by carefully heating with a heat gun.
23. Palladium(II) acetate (Pd(OAc)2 (recrystallized, 97%)) was obtained from
Sigma-Aldrich and was used as received.
24. Care should be taken to carefully pour the material into the middle of the
vortex to ensure that it is readily taken up by the melt and does not
remain floating upon the surface.
25. The melt became pale brown with a few remaining undissolved particles
of Pd(OAc)2.
26. In the event that 2 was obtained as thick plates, the solid was finely
ground using a mortar and pestle before addition.
27. Completion of the reaction occurred rapidly after dissolution of the
starting material 2 into the melt. The submitters recommend to monitor
the reaction by performing TLC-analyses every two minutes after the
addition of 2. A sample is taken by putting the tip of a glass pipette into
the hot reaction mixture and the black residue remaining on the glass
pipette is diluted with EtOAc and then used for TLC monitoring. Thin-
layer chromatography was performed using silica gel 60 F254-plates from
Merck, Darmstadt, Germany and a 9:1 mixture of CH2Cl2/MeOH as
eluent. The starting material 2 shows an Rf value of 0.91, whereas the
desired product 3 shows an Rf value of 0.46 (both visible under UV light)
(Figure 9).

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 Figure 9. TLC monitoring of the Heck reaction immediately after
adding 2 (left plate) and 5 min after the addition (right plate). Left
lanes: starting material 2; Right lanes: reaction mixture diluted with
EtOAc; middle lanes: co-spot. CH2Cl2/MeOH (9:1) used as eluent
(photos provided by submitters)

28. The submitters wrapped paper towels around the beaker to facilitate
pouring of the hot melt. This also assures that no oil sticking to the
outside of the beaker is unintentionally transferred into the reaction
mixture.
29. Celite Standard Super Cel was obtained from Carl Roth and was used as
received.
30. The tetrabutylammonium salts don’t exclusively partition into the
aqueous layer when using EtOAc as an organic solvent, which
necessitates multiple washes. The submitters suggest monitoring the
organic layer for the presence of remaining salts by thin-layer
chromatography (TLC) (CH2Cl2/MeOH 9:1). The salts appear as a
streaky spot (visible with I2 stain, but not UV) below the product spot
(visible under UV and with I2 stain). Washing should be repeated
(usually 5–7 times) until no further tetrabutylammonium salts can be
detected (Figure 10).

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 Figure 10. TLC monitoring of the washing procedure with H2O. From
left to right lane: organic layer after the first phase separation, then
after the next six aqueous washes; CH2Cl2/MeOH 9:1 used as eluent;
TLC plate is stained with iodine (photos provided by submitters)

31. Accurate phase separation is occasionally difficult due to cloudiness and

bubble formation between the layers. The submitters prefer to keep a
minimal amount of water in the funnel during each separation so as not
to lose product during the washing procedure.
32. After the washing is complete, a small volume of the organic phase is
removed and concentrated on a rotary evaporator (40 °C, 6 mmHg). The
residue is analyzed by 1H NMR spectroscopy in order to determine the
ratio of desired product 3 and its aromatized isomer 6 (Figure 11 and see
Discussion). This ratio varies between 5:1–8:1 (diagnostic signal marked
with red circle: desired product 3, 5.30 ppm; aromatized byproduct 6,
5.53 ppm in CDCl3).

Figure 11. Products arising from Heck reaction of iodoimidazole 2

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33. Sodium hydroxide was obtained from VWR Chemicals Prolabo and was
used as received.
34. These washes remove hydroxybenzimidazole 6 from the organic layer by
deprotonating the hydroxyl group and helping to partially partition 6
into the aqueous layer. Ketone 3 also partially partitions into the aqueous
layer during this procedure, but material loss is minimal. That both
products partition into the aqueous phase is seen visually as depicted in
Figure 3C: Upon standing for a few minutes at 24 °C, a fine off-white
solid (3 and 6) precipitates from the aqueous phase.
The washing procedure can be monitored by thin-layer chromatography
using silica gel 60 F254-plates from Merck, Darmstadt, Germany and
benzene/MeOH (9:1) as eluent (Figure 12). Byproduct 6 appears as a
slightly faster eluting spot than 3 under these conditions. Small quantities
of byproduct 6 visualize very well under UV and with I2 staining, making
it difficult to determine when to stop washing. The submitters have
found that 10 washes consistently provide sufficiently pure samples of 3
(also see discussion), and recommend using this number of washes, but
still monitoring via TLC for a visual analysis. After the 10 washes, a small
volume from the organic phase can be concentrated and analyzed by 1H
NMR. If a 3/6 ratio ≥50:1 is not obtained after 10 washes, further washing
with 1M NaOH must be performed.

Figure 12. TLC monitoring of the basic washing procedure with 1M

NaOH. From left to right lane: pure product 3 obtained in a different
experiment, organic phase from 1st to 5th wash (left TLC plate) and
organic phase from 6th to 10th wash (right TLC plate), benzene/MeOH
9:1 used as eluent; TLC plate is stained with iodine (photos provided
by submitters)

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35. Activated carbon was obtained from Sigma-Aldrich and was used as
received.
36. Treatment of the organic phase with charcoal was done to decolorize the
product by removing trace impurities such as palladium.
37. The submitters adopted this precipitation procedure due to difficulties in
removing all traces of EtOAc from 3 when it was concentrated to a solid
from an EtOAc solution, even after the resulting solid was dried at 100 °C
under high vacuum for 24 h. This precipitation method reliably provided
solvent-free 3 after drying the filtered solid under high vacuum.
38. If the product re-dissolves during concentration, the flask should be
removed from the rotary evaporator and additional n-hexane should be
added, to ensure that the product remains a solid throughout this
process.
39. The majority of the solid can be scratched out of the flask with a spatula
and transferred to the funnel by rinsing with n-hexane. Any solid
remaining in the round-bottomed flask is negligible, but if a quantitative
transfer is desired, it can be redissolved in EtOAc, transferred into a
smaller (100 mL) round-bottomed flask, concentrated on a rotary
evaporator (40 °C, 150 to 35 mmHg) to a solid, and then transferred to the
Büchner funnel.
40. To ensure complete removal of trace EtOAc, the solid was crushed in the
funnel with a spatula, then covered with n-hexane, the resulting
suspension was well mixed with the spatula, and then vacuum was
applied to pull the solvent through the funnel. This procedure was
repeated (3-4 times) until 500 mL of n-hexane were consumed.
41. The product (3) exhibits the following analytical data: Rf = 0.46
(CH2Cl2/MeOH 9:1) and 0.19 (benzene/MeOH 9:1). mp (uncorrected):
147.0–149.0 °C. 1H NMR (600 MHz, CDCl3) δ: 2.70 (t, J = 6.6 Hz, 2H), 2.81
(t, J = 6.0 Hz, 2H), 5.13 (s, 1H), 5.26 (s, 1H), 5.33 (s, 2H), 7.08 (d, J = 7.2 Hz,
2H), 7.35 – 7.40 (m, 3H), 7.57 (s, 1H). 13C NMR (151 MHz, CDCl3) δ: 34.1,
38.6, 49.7, 112.2, 126.3, 128.4, 129.3, 132.9, 134.9, 138.0, 139.4, 141.9, 191.5.
Purity was determined to be 89.6% by qNMR spectroscopy in CDCl3
using 23.9 mg of compound (3) and 10.7 mg of dimethyl sulfone (99.65%)
as an internal standard. LC-MS (M+H) calcd for C15H15N2O (m/z): 239.
HRMS–ESI (m/z) (provided by submitters): [2M + Na]+ calcd for
C30H28N4NaO2+: 499.2104, found: 499.2109.
42. While 3 obtained via this extractive purification is 89.6% pure (based on
qNMR), a sample that is entirely free of 6 and other minor impurities can

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 be prepared by crystallization: a sample of 3 (1.0 g, 4.19 mmol) is
dissolved in hot EtOAc (~40 mL) on a water bath (100 °C), filtered while
hot, and n-hexane (~15 mL) is then added while the solution is still on the
water bath until the white precipitate which forms only slowly
disappears. The mixture is cooled to 24 °C and then to –20 °C for 18 h.
After filtration through a round paper filter (ø = 5.5 cm) using a Büchner
funnel, washing with cold (4 °C) EtOAc/n-hexane 1:1 (13 mL) and then
cold (4 °C) n-hexane (2 x 15 mL), and air drying for 1 h on the filter using
house vacuum, an off-white solid (0.774 g, 3.23 mmol, 77.4%) was
obtained (Figure 13). 1H NMR (600 MHz, CDCl3) δ: 2.70 (t, J = 6.6 Hz,
2H), 2.81 (t, J = 6.0 Hz, 2H), 5.13 (s, 1H), 5.26 (s, 1H), 5.34 (s, 2H), 7.08
(d, J = 7.2 Hz 2H), 7.33 – 7.40 (m, 3H), 7.57 (s, 1H). 13C NMR (151 MHz,
CDCl3) δ: 34.1, 38.6, 49.7, 112.2, 126.3, 128.4, 129.3, 132.9, 134.9, 138.0,
139.4, 141.9, 191.5. Purity was determined to be 96.8% by qNMR
spectroscopy in CDCl3 using 24 mg of compound (3) and 9.7 mg of
dimethyl sulfone (99.65%) as an internal standard.

Figure 13. Pure 3 obtained by crystallization from hot EtOAc/n-hexane

43. The submitters obtained an analytical sample of aromatized byproduct 6

as follows: The aqueous phases of the basic washing procedure (see
Note 34) are combined and acidified by dropwise addition of
concentrated HCl to pH~5–6. Then the aqueous phase is extracted with
EtOAc (3 x 200 mL), whereupon the combined organic phases are
washed with brine (300 mL) and concentrated on a rotary evaporator
(40 °C, 280 to 15 mmHg). The obtained brown solid is suspended in hot
EtOAc (50 mL). The suspension is filtered using a fluted filter paper in a
250 mL round-bottomed flask, and to the hot solution of EtOAc is added

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 n-hexane (50 mL). The flask is covered with a plastic cap (wrapped with
Parafilm) and allowed to cool to 24 °C on the bench and then at –20°C in
a freezer. The resulting yellow solid is filtered through a round filter
paper (ø = 4.5 cm) using a Büchner funnel and washed with a minimum
amount of cold (4 °C) EtOAc/n-hexane 1:1 (20 mL) and then cold (4 °C)
n-hexane (2 x 20 mL) and air dried on the filter for 1 h using house
vacuum (Figure 14).

Figure 14. Appearance of aromatized byproduct 6 (photo provided by

submitters)

The aromatized byproduct 6 exhibits the following analytical data

(provided by the submitters): Rf = 0.46 (CH2Cl2/MeOH 9:1) and
0.30 (benzene/MeOH 9:1). mp (uncorrected) 207–209 °C
(decomposition). 1H NMR (400 MHz, DMSO-d6) δ 2.26 (s, 3H), 5.64 (s,
2H), 6.44 (d, J = 7.8 Hz, 1H), 6.67 (dd, J = 7.9, 1.0 Hz, 1H), 6.92 – 6.98 (m,
2H), 7.20 – 7.37 (m, 3H), 8.15 (s, 1H), 9.57 (br. s, 1H). 13C NMR (101 MHz,
DMSO-d6) δ 17.4, 48.8, 106.5, 111.7, 125.2, 125.6, 127.5, 128.9, 133.9, 134.1,
139.2, 144.0, 147.6. HRMS–ESI (m/z): [2M + Na]+ calcd for C30H28N4NaO2+:
499.2104, Found: 499.2110.

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330
Working with Hazardous Chemicals

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Discussion

We required an efficient synthesis of ketone 3 and related substances for

a project devoted to the synthesis of covalent methionine aminopeptidase 2
(MetAP2) inhibitors. Our first-generation library of substances were
spiroepoxyimidazoles 7, which were all synthesized from 1 via alkylation,
Heck cyclization, and epoxidation with DMDO (Figure 15A). The
compounds were designed to mimic the natural product ovalicin, a potent
and selective covalent MetAP2 inhibitor (Figure 15B). Our second-generation
inhibitors were based on a triazole scaffold, and we found them to be more

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331
potent and to have better physicochemical properties than the imidzoles
(Figure 15C).2

Figure 15. (A) Synthesis route to 1st generation MetAP2 inhibitors; (B)
Small library of putative MetAP2 inhibitors inspired by ovalicin; (C)
General structure of 2nd generation MetAP2 inhibitors

Outside of the context of our MetAP2 inhibitor project, compound 3 is an

interesting building block due to the fact that it can potentially be derivatized
in a variety of ways to generate a diverse collection of substances (Scheme 1).
Besides oxidation to epoxide 7 as mentioned above, ketone 3 can also be
transformed to aziridines 8,3 undergo reductive amination to give amines 9,4
or reduced to alcohol 10.5 Alternatively, the exocyclic double bond can be
reduced to a methyl group to afford ketone 11,6 or undergo Huisgen
cycloaddition reactions with 1,3-dipoles to afford spirocycles of type 12.7
Many more manipulations can also be envisaged, including those that
involve removal of the benzyl group and replacement with other
substituents.8

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332
 Scheme 1. Some possible transformations with annulated imidazole 3

We now discuss some noteworthy details from our explorations into the
synthesis of 3. In the first step, iodoimidazole 1 is alkylated with benzyl
bromide. Because the two imidazole nitrogens in 1 are regiotopic, two
products (2 and 4) can be expected and, indeed, are formed in the mono-
benzylation reaction (Scheme 2).

Scheme 2. Reaction of 1 with benzyl bromide produces

two regioisomeric products

We investigated the influence of temperature, solvent, base, and

electrophile on the reaction and found benzyl bromide with K2CO3 in DMF
to give a clean, rapid conversion to the two products. Conducting the reaction

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333
at 0 °C gave the most consistent product ratios, with 2 and 4 formed in a ratio
between 6:1 and 8:1. Because 2 is purified by crystallization, the resulting
mother liquor is highly enriched in 4. We speculated that if the product ratio
obtained in the initial reaction reflected a thermodynamic ratio, we could
potentially equilibrate the mother liquor mixture, via the intermediacy of the
corresponding dibenzylated imidazolium salt (5), by heating with a catalytic
amount of benzyl bromide (Scheme 3).9 Attempts to perform such an
equilibration revealed that 5 forms readily and is quite stable; therefore, no
equilibration occurred. Moreover, running the initial benzylation reaction
with larger equivalents of benzyl bromide (e.g. 1.2 equiv), even at lower
temperatures, results in significant imidazolium salt formation. Compound 5
is highly crystalline and can cause problems during the crystallization of 2
(see Notes 11 and 13). Therefore, the submitters advise using only a slight
excess of benzyl bromide (1.01–1.05 equivalents) for the alkylation of
imidazole 1.

Scheme 3. Envisioned equilibration of 2 and 4 via imidazolium salt 5

The subsequent intramolecular Heck cyclization with 2 proved

challenging. Our initial attempts with “typical” Heck conditions, showed that
only ligandless Jeffery conditions (Pd(OAc)2, (n-Bu)4NBr, Na2CO3,
MeCN/H2O, 70 °C) resulted in any reaction. However, long reaction times
(several days) and multiple catalyst loadings were required to obtain useful
quantities of product, and we never observed complete consumption of the
starting material. We were, therefore, extremely pleased to find that the
method of Nacci and co-workers,11 which employs palladium
colloids/nanoparticles in an ionic liquid of (n-Bu)4NBr and (n-Bu)4NOAc at
130 °C worked extremely well, with full conversion of the starting material
in less than 10 minutes.
In addition to the desired product 3, we observed its aromatized
tautomer hydroxybenzimidazole 6 as a byproduct, typically with a 3/6 ratio
between 5:1 and 8:1 (Scheme 4). We were pleased that 3 was stable enough to

Org. Synth. 2021, 98, 315-342 DOI: 10.15227/orgsyn.098.0315

334
be isolated, but were concerned that isomerization of 3 to 6 was taking place
during the reaction. If this was the case, small changes in the time spent in
the reaction melt at 130 °C could produce variable product ratios. To
investigate our concerns, we treated pure 3 under both strongly basic and
acidic conditions, and found essentially no isomerization. We also found that
performing the Heck reaction for longer reaction times, or under an inert
anhydrous atmosphere, or with an added 10 equivalents of water had no
effect on the 3/6 product ratio. We also re-subjected pure 3 to the reaction
conditions for 1 h, but no 6 was detected by NMR of the reaction mixture
upon work-up.

Scheme 4. Heck reaction of iodoimidazole 2 affords the desired product (3)

(X-ray structure)12 and its aromatized congener (6). Ellipsoids for 3 are
shown at a 50% probability level; carbon: gray, nitrogen: blue, oxygen: red

Since the 3/6 ratio is unaffected by the presence of air or water, and 3
does not isomerize under the reaction conditions, we postulate that 6 is
formed via a side reaction involving the intermediate palladium hydride
species formed during the Heck reaction. The catalytic cycle starts with the
oxidative addition of Pd(0) (Pd(OAc)2 can be reduced to Pd(0) under these
conditions to form colloids/nanoparticles, which are productive Heck
catalysts)13 into the I--Ar bond of 2 to form 13 (Scheme 5). After coordination,
Pd(II) inserts into the double bond, giving intermediate 14. -Hydride
elimination forms the expected product 3 and H-Pd-I. Reductive elimination
of the latter regenerates the catalyst Pd(0), and produces HI, which is
sequestered by acetate.

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335
Scheme 5. Catalytic cycle of Heck reaction with iodoimidazole 2 affording
product 3 (including postulated reaction path to hydroxybenzimidazole 6)

If H-Pd-I re-inserts into 3 before undergoing reductive elimination,

intermediate 15 could be formed.14 A subsequent “productive” syn-b-hydride
elimination from 15 would yield 16, and after keto-enol tautomerization,
hydroxybenzimidazole 6. Compound 6, due to its extended aromaticity, is
assuredly more thermodynamically stable than 3 and will not revert to 3. This
mechanistic explanation for the conversion of 3 into 6 can only take place in
the presence of a palladium hydride species, and is consistent with our
observations, i.e. after consumption of the starting material (or if no starting
material is present to begin with), palladium hydride species should not be
formed, and isomerization of 3 to 6 cannot take place.

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336
 Isomers 3 and 6 are almost co-polar by TLC under all solvent systems
that we tested, making chromatography ineffective as a means of purification.
Crystallization was also problematic, due to the relatively low solubility and
high crystallinity of 6. We, therefore, employed a basic extraction procedure,
which enabled enrichment of 3 in the organic phase due to the relatively low
pKa of hydroxybenzimidazole 6. In one full-scale run of this reaction, we
quantified the success of the extraction procedure by taking aliquots of the
organic phase after the first, third, fifth, seventh and tenth washing step (see
Note 34). These were concentrated on a rotary evaporator and measured by
NMR to evaluate the 3/6 ratio at each step of this procedure. As can be seen
in Figure 16, 10 washes were sufficient to bring the content of 6 to ~2%.
Because each basic wash also leads to a loss of desired product 3 (monitored
by TLC of the aqueous phase), the washing procedure should be stopped
after ten cycles.

12
A m t . o f 6 r e m a in in g ( % )

10

0
0 5 10

N um ber of w ashes

Figure 16. Product ratio 3/6 in the organic phase throughout the basic wash
as determined by NMR in table and graph formats

References

1. Cancer Drug Development Group, German Cancer Research Center

(DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
E-mail: [email protected]. ORCID for MM: 0000-0001-9539-6404;
ORCID for AKM: 0000-0002-1761-4143; The Helmholtz Drug Initiative is
gratefully acknowledged for financial support. We thank Frank
Rominger (Organic Chemistry Institute, Heidelberg University) for X-ray
data of compound 3.

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337
2. (a) Miller, A.; Jöst, C.; Klein, C.; “Preparation of spiroepoxide
tetrahydrobenzotriazoles and -imidazoles useful as MetAP-II-
inhibitors”, Eur. Pat. Appl. (2014), EP 2711367, A1 20140326. (b) Morgen,
M.; Jöst, C.; Malz, M.; Janowski, R.; Niessing, D.; Klein, C. D.; Gunkel, N.;
Miller, A. K. ACS Chem. Biol. 2016, 11, 1001–1011.
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D.; Ess, D. H.; Kürti, L.; Falck, J. R. Science 2014, 343, 61–65.
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Compounds and Methods for the Preparation thereof”, WO 99/27783
(PCT/US98/25624).
5. (a) Kirmse, W.; Rode, K. Chem. Ber. 1987, 120, 839–846. (b) Fairhurst, R.
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J. J. Org. Chem. 1978, 43, 4194–4196. (b) Haddach, A. A.; Kelleman, A.;
Deaton-Rewolinski, M. V. Tetrahedron Lett. 2002, 43, 399–402. (c) Graham,
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13. (a) Calò, V.; Nacci, A.; Monopoli, A. Eur. J. Org. Chem. 2006, 3791–3802.
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Appendix
Chemical Abstracts Nomenclature (Registry Number)

1-(5-Iodo-1H-imidazol-4-yl)pent-4-en-1-one: 4-Penten-1-one, 1-(5-iodo-1H-

imidazol-4-yl)-; (1585257-59-5)
Potassium carbonate: Carbonic acid, potassium salt (1:2); (584-08-7)
Benzyl bromide: Benzene, (bromomethyl)-; (100-39-0)
1-(1-Benzyl-5-iodo-1H-imidazol-4-yl)pent-4-en-1-one: 4-penten-1-one, 1-[5-
iodo-1-(phenylmethyl)-1H-imidazol-4-yl]-; (1585257-17-5)
Palladium(II) acetate: Acetic acid, palladium(2+) salt (2:1); (3375-31-3)
Tetra-n-butylammonium bromide: 1-Butanaminium, N,N,N-tributyl-,
bromide (1:1); (1643-19-2)
Tetra-n-butylammonium acetate: 1-Butanaminium, N,N,N-tributyl-, acetate
(1:1); (10534-59-5)
1-Benzyl-7-methylene-1,5,6,7-tetrahydro-4H-benzo[d]imidazole-4-one: 4H-
Benzimidazol-4-one, 1,5,6,7-tetrahydro-7-methylene-1-(phenylmethyl)-;
(1585257-23-3)

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 Michael Morgen received his Ph.D. in inorganic
chemistry from the Ruprecht-Karls-University,
Heidelberg in 2013 while working with Prof. Dr.
Peter Comba on the design of novel bispidine-
based multimodal imaging agents. Afterwards he
joined the Cancer Drug Development Group of Dr.
Aubry Miller and Dr. Nikolas Gunkel at the
German Cancer Research Center (DKFZ). His
current research interests lie in the design and
synthesis of organic and metal-organic inhibitors
for cancer-related drug targets.

Jasmin Lohbeck was trained as chemistry

laboratory assistant at BASF in Ludwigshafen,
Germany, from 2006 – 2009. She subsequently
joined the chemistry lab of Dr. Aubry Miller at the
German Cancer Research Center and specialized in
preparative organic synthesis.

Aubry Miller leads the Cancer Drug Development

Group at the German Cancer Research Center
(DKFZ) in Heidelberg, Germany. His laboratory
focuses on the discovery and biological
characterization of chemical probes for use as tools
and drug leads in cancer research.

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340
 Nageswara Rao Kalikinidi earned his Ph.D. in 2018
in Synthetic Organic Chemistry from the CSIR-
IICT, India, under the guidance of Dr. Subhash
Ghosh. His research focused on developing a
synthetic route for the total synthesis of
biologically active and architecturally complex
marine natural products. In 2019, he joined in Prof.
E. J. Corey research group at Harvard University,
where his research was focused on the
enantioselective epoxidation reactions with chiral
azatetracycle catalysts. After completing his
postdoctoral studies in 2021, Nageswara joined
TCG GreenChem, Inc. as a post-doctoral Scientist.
His research interests include the design and
development of green and robust large-scale
production of active pharmaceutical ingredients
(APIs) and synthetic methodology of novel organic
transformations using chiral phosphine ligands.

Venumadhav Janganati earned his Ph.D. in

synthetic organic chemistry from National
Institute of Technology, Warangal, India in 2009
under the guidance of Prof. B. Rajitha. His research
focused on synthesis of bioactive heterocyclic
molecules and developing novel methodologies by
using new reagents. In his postdoctoral training at
the University of Arkansas for Medical Sciences,
USA, he designed and synthesized natural product
(parthenolide) derivatives for anti-cancer therapy,
and he was also involved in design and synthesis
of lobelane derivatives, which focused on the
development of new treatments for
methamphetamine addiction. Currently working
as a senior scientist in Process Chemistry at TCG
GreenChem, Inc., his research interests include the
process research and development and
asymmetric catalysis.

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341
 Dr. Gopal Sirasani received his Bachelor’s and
Master’s degrees in Hyderabad, India. He obtained
his Ph.D. in synthetic organic chemistry in 2011
from Temple University, Philadelphia under the
guidance of Prof. Rodrigo B. Andrade. His doctoral
research focused on developing novel
methodologies, total syntheses of natural products
and their analogs thereof. He got his post-doctoral
training in the laboratory of Prof. Emily Balskus at
Harvard University, where he developed
biocompatible organic reactions utilizing
microbially generated reagents to realize transition
metal catalysis in the presence of microbes. In 2013,
Gopal began his industrial career at Melinta
Therapeutics, New Haven, CT. He is currently
working at TCG GreenChem, Inc. as a Director in
the department of process research and
development.

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 NMR data for step A of Org Syn#3638
1
H NMR spectrum of product of step A in DMSO-d6
13
C NMR spectrum of product of step A in DMSO-d6
Q-NMR spectrum of product of step A in DMSO-d6
 NMR data for step B of Org Syn#3638
1
H NMR spectrum of compound 3 in CDCl3
13
C NMR spectrum of compound 3 in CDCl3
 qNMR spectrum of compound 3

The purity was confirmed by qNMR spectroscopy in CDCl3 using 23.9 mg of compound (3) and 10.7 mg of Dimethyl sulfone
(99.65%) as an internal standard.
 I sample N standard M sample m standard
P sample = ∗ ∗ ∗ ∗ P standard
I standard N sample M standard m sample
0.7935 6 238.29 10.7
= ∗ ∗ ∗ ∗ 99.65%
6.0000 1 94.13 23.9
= 89.61%
After recrystallization: 1H NMR spectra
After recrystallization: 13C NMR spectra
After recrystallization: qNMR spectra

The purity was confirmed by qNMR spectroscopy in CDCl3 using 24 mg of compound (3) and 9.7 mg of Dimethyl sulfone (99.65%)
as an internal standard.
 I sample N standard M sample m standard
P sample = ∗ ∗ ∗ ∗ P standard
I standard N sample M standard m sample
0.95 6 238.29 9.7
= ∗ ∗ ∗ ∗ 99.65%
6.0000 1 94.13 24
= 96.8%