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Bachelor Thesis

Chemistry

Synthesis of [2]rotaxanes containing endocyclic quinones

by

Akshay Sadhoe 12004138

24 August 2020

Research institute

Daily supervisor

FNWI

Nick Westerveld

Research group

Supervisor

Synthetic Organic Chemistry

Prof. Dr. Jan H. van Maarseveen

Second examiner

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Introduction

The development of transition metal reagents and catalyst have received a lot of attention in order to perform redox reactions, such as the production of H2O2 and the generation of H2 gas.1,2 These

types of oxidation reactions are crucial in the chemical industry, since they produce valuable resources.2 Other redox reactions utilizing inorganic reagents include redox flow batteries, of which

researchers have tried to replace redox couples of M3+ and M2+, as they are usually toxic and

expensive.3 Replacing these types of toxic and expensive reagents are prominent challenges in the

chemical industry. Furthermore, redox active organic compounds can also be potent catalysts, meaning that the challenges are feasible, for example the use of 2,2,6,6-tetramethylpiperidine N-oxyl and phthalimide N-oxyl for alcohol oxidation and autoxidation reactions respectively.4,5 Since nature

also uses organic compounds in order to catalyze redox reactions, such as quinones, they could be outstanding candidates. Furthermore, these quinones could be better candidates than some metal-based redox couples, due to their high energy density.6

Quinones are a class of molecules that are oxidized derivatives of organic compounds containing a fully conjugated cyclic dione structure.7 The 1,4-benzoquinone is often called the quinone, however,

quinones have other archetypes as well, such as 1,2-benzoquinone which is called ortho-quinone, 1,4-naphtaquinone and 9,10-anthraquinone (Figure 1).8 These quinone archetypes have diverse

applications for energy harvesting and storage, such as artificial photosynthesis, pseudocapacitors, rechargeable batteries, phototransistors, dye-sensitied solar cells and light harvesting platforms.9

Figure 1. Quinones and their archetypes.8

These quinones have several species, which can be reached after one or two-electron reductions of the quinone, of which the one-electron reduction leads to the semiquinone and the two-electron reduction leads to the hydroquinone (Figure 2).8 Quinone species have important roles in energy

transport and serve mostly as vital parts in electron transport, since they can be used for two-electron reduction.10 Their redox behaviour has an important role in electrochemical reactions. For

example in photosynthesis, where the chemical energy is generated through photoinduced electron transfer reactions. The key redox mediators in these photosynthetic units are usually primary and secondary quinones, where the quantum yield is extremely high, meaning that the quinones seem to be very efficient redox mediators.9

Figure 2. Redox cycling of 1,4-benzoquinone to the semiquinone and hydroquinone species.8

Quinones like these could also be integrated in rotaxanes, resulting in molecules that could be used as catalysts. Rotaxanes have been used for catalysis before by placing a catalytic motif on a rotaxane scaffold, to achieve high selectivity and yield.11 For example the utilization of chiral rotaxanes to

catalyze asymmetric benzoin condensation by Tachibana et al.12 Another great utilization of rotaxane

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rotaxane for the formation of C–C and C–S bonds and have shown that they could control the reaction rate. Their catalytic rotaxane could be switched ‘’on’’ and ‘’off’’ through

acid/base-promoted translocation of the macrocycle on the axle which would reveal or conceal the active site, effectively controlling the rate of the reaction.13 These findings suggest that the rotaxane scaffold can

greatly influence the reaction which is promoted by the catalytic motif by opening up new mechanistic pathways, increasing the selectivity and control.

However, in our situation when integrating quinones into the rotaxane scaffold, the catalytic motif should still be redox active. Meaning that the redox cycling between quinone and hydroquinone is reversible while integrated into the rotaxane, which can be confirmed using cyclic voltammetry.14

The rotaxanes to be synthesized in this paper are portrayed in Figure 3, which show a 26-atom and a 30-atom rotaxanes. The 30-atom ring is a larger ring and will be more likely to succeed in the Glaser-coupling, but the 26-atom ring is also interesting since it allows for smaller stoppers, so both of them will be synthesized.

Figure 3. The quinone integrated rotaxanes to be synthesized.

Rotaxanes have several methods of synthesis, including clipping capping and covalent template synthesis. The clipping method involves the thread to be stoppered, after which the unsealed macrocycle binds to it and is sealed, resulting in the wanted rotaxane. During the capping method the macrocycle is already sealed and the thread has to pass through, after which it is stoppered. The covalent template synthesis has two unsealed macrocycle precursor units that are covalently bound to the thread, after which the macrocycle is sealed, the thread is stoppered and finally the bond between the thread and the macrocycle is cleaved.15

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Firstly, the template and the macrocycle precursor will be synthesized, after which the macrocycle precursor is coupled to the template. Hereafter, a Glaser-Eglinton reaction is performed for the ring closure and the product is reduced to end up with the pre-rotaxane (Figure 4). The reaction following up will be the synthesis of the stoppers, after which the stopper is attached to the pre-rotaxane (Figure 5). Finally, the bonds linking the macrocycle to the thread will have to be cleaved, which will be done using CAN (ceric ammonium nitrate).

The research will focus on the synthesis of rotaxanes containing endocyclic quinones, which will be done through a covalent template synthesis method.16 The central question is whether the

Glaser-Eglinton coupling of the terminal alkynes is able to seal the ring and what conditions should be used in this reactions.

Figure 4. Synthesis scheme of the pre-rotaxane, with A: n = 1 and B: n = 2.

Figure 5. Attachment of the stopper and cleaving of the ester bond utilizing CAN, with A: n = 1 and B: n = 2.

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Results & discussion

Figure 6. Synthesis of the terephthalic template.

The synthesis of the terephthalic template 5 began by reducing 1, utilizing N-chlorosuccinimide (NCS) in order to get the di-phenol 2 in 82% yield. Hereafter, the double allylation of 2 was performed using and allyl bromide in presence of potassium carbonate, resulting in 3 with a yield of 66%. The double allylation was followed by the saponification of 3, using potassium hydroxide yielding in 75% of di-acid 4. 4 was then esterified, using pentafluorophenol in the presence of N, N-diisopropylethylamine (DIPEA) which resulted in bispentafluorophenyl ester 5 with a yield of 58% (Figure 6).

Figure 7. Synthesis of the macrocycle precursor, with A: n = 1 and B: n = 2.

The synthesis of macrocycle precursor 8B commenced with double hydroxymethylation of 1,4-methoxyphenol with formaldehyde in presence of sodium hydroxide, resulting in triol 6 with a yield of 93%. The double hydroxymethylation was followed by double bromination of the benzylic hydroxyl groups, utilizing hydrogen bromide in acetic acid which yielded in 37% of dibromide 7 (Figure 7).

Hereafter, organohalide 7 was used for Williamson ether synthesis, utilizing but-3-yn-1-ol in presence of sodium hydride to give benzylic diether 8B with a yield of 23%. This reaction was tried multiple times in order to improve the yield. Adding 7 in one portion was compared to dropwise adding 7 dissolved in dry THF through a dropping funnel to minimize any polymerization that might take place, however, no increase in yield was observed when adding 7 slowly. Another observation in the

Williamson reaction was that the triple bond in 8B could isomerize in presence of a strong base, such as sodium hydride, shifting the triple bond between different carbon atoms on the alkyl chain (Figure 8), which suggests that the reaction should not be stirred for too long. This was confirmed using 1

H-NMR, where the peaks of the compounds with shifted triple bonds could be seen, also, TLC showed 3 stacked spots which were very difficult to separate column chromatography on small scale, indicating isomerization. The 1H-NMR shown in Figure 8 is taken from a mixture of 8B and isomerized product

from a reaction that was stirred for five days. The peaks at 4.67–4.65 are from the hydrogen atoms marked with blue arrows in Figure 8, and were chosen for comparing since all three isomers have these peaks with the same amount of hydrogen atoms, giving the possibility to use the integrals of these peaks quantitatively. These hydrogen atoms were also chosen, since they are the closest to the ether chain, which isomerizes. Notable is that the peaks at 4.67, 4.66 and 4.65 ppm are three

separate singlets with integrals of 1.59, 1.59 and 0.63 respectively, while the pure product shows only one singlet at exactly the 4.65 ppm with an integral of 4H. Since the peak at 4.65 has the lowest

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integral, it suggests that the majority of the product had isomerized. Furthermore, when comparing the 1H-NMR of 8B and the 1H-NMR of the mixture of isomers, it can be seen that small traces of

peaks of the mixture can be found in the NMR of 8B (marked orange in Figure 9), which indicates traces of isomers were present in the product, suggesting that isomerization did take place.

However, assignment was not possible since the coupling patterns of the orange marked peaks in the isomer mixture were very complicated.

Figure 8. The triple bond shift of compound 8B.

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Figure 10. Synthesis of the Glaser-coupled product, with A: n = 1 and B: n = 2.

After the synthesis of the terephthalic template 5 and the macrocycle precursor 9B, the next step was to couple two macrocycle precursor fragments with one template unit, which was done in dry acetonitrile in presence of caesium carbonate, resulting in 9B with a yield of 81%. Hereafter, the allyl groups on 9B were cleaved, using diethylamine with Pd(PPh3)4 in dry 1,4-dioxane, which yielded in

53% of 10B (Figure 10).

The following step was the Glaser-Eglinton coupling of the terminal alkynes to get compound 11B, which was tried starting with both 9B and 10B, in order to see whether the allyl group has any influence on the coupling reaction (Figures 10 and 11). The reaction utilized copper chloride with tetramethyl ethylenediamine (TMEDA). Unfortunately, no product could be recovered from the reaction starting with 9B, however, crude 1H-NMR showed that the reaction did have conversion.

Peaks of both starting material and product were observable in the crude NMR. There seemed to be a slight shift of the peaks from the starting material (SM) with integrals that were either 2:1 SM: product (P) or 1.5:1 SM:P, suggesting that the reaction had a conversion between 30 and 40%. However, the reaction was performed on 40 mg scale, resulting in no product being isolated due to the low conversion.

Figure 11. The Glaser-Eglinton coupling tried with compound 9B, with A: n = 1 and B: n = 2.

The reaction was also performed starting from 10B, using the same conditions as the reaction starting from 9B. However, this reaction had no conversion at all, which might have happened due to catalyst poisoning. The order in which chemicals were added could have played a role in this. At the time of setting up the reaction 10B was added first, after which TMEDA in THF and copper chloride were added in sequence. The TMEDA could have deprotonated the phenols in 10B, after which the phenoxide would attach to the copper chloride, effectively poisoning the catalyst. A better sequence

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to add the chemicals would be TMEDA and copper chloride first in THF, after which 10B in THF is added dropwise to the reaction mixture, so the TMEDA does not deprotonate the phenols and to limit the extent of any polymerisation of 10B which might take place. A paper from Fomina et al. also highlights the mechanism of the Glaser coupling, utilizing DFT calculations.17 It was found that in the

initial steps the alkyne and TMEDA form a complex with the copper atom, which facilitates the acetylenic proton abstraction. This proton abstraction can be both intra- or intermolecular, of which was found that the intermolecular proton transfer is more favourable kinetically and

thermodynamically, meaning that another tweak to the Glaser coupling might be using twice as much TMEDA, since two TMEDA molecules are needed for intermolecular proton abstraction. However, due to lack of time these tweaks could not yet be implemented in the coupling, but might be used in the near future to try and improve the yield. Furthermore, since the reaction has such a low energy barrier that it can be performed at room temperature, a higher temperature could also be tested.

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Conclusion & outlook

Due to the lack of time the last reaction that could be performed was the Glaser-Eglinton coupling. However, it was shown that the reactions regarding the synthesis of the terephthalic template went well and gave decent yields. Notable of the macrocycle precursor synthesis was the Williamson ether synthesis, where the product was able to isomerize when stirred for too long in presence of a strong base such as sodium hydride. The coupling reaction gave good yield as well but, the following Glaser coupling does need some tweaking in order to give a decent yield. Some things that could be tried for tweaking the Glaser coupling are using twice as much TMEDA, since the more favourable

intermolecular proton abstraction would require another TMEDA unit, which could speed up the reaction. Also, whether the sequence of adding the chemicals in the Glaser coupling has any influence on catalyst poisoning should be investigated, since it might lead to improved yields. However, due to the Glaser-coupling reactions not producing any yield, no clear conclusion can be drawn on whether the coupling works in our case, since there are still tweaks on the reactions to be tried. For further research the synthesis of the rotaxanes could be finished and the reversibility of their redox cycling should be investigated using cyclic voltammetry.

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Experimental section

Synthesis of compound (2): 1 (10.4 g, 50 mmol, 1 eq) was mixed with acetic acid (50 mL). The mixture

was heated to 80 °C, after which N-chlorosuccinimide (6.8 g, 50 mmol, 1 eq) was added portion wise over 30 mins. The mixture was stirred for another 90 mins at 80 °C. The mixture was then allowed to cool down to room temperature, after which water (50 mL) was added. The solid was vacuum filtrated and washed on the filter with water (3 x 25 mL) and cold methanol (3 x 5 mL), which yielded in 9.25 g of compound 2. (82% yield)

Figure E1. 1H-NMR of compound 2.

1H-NMR (400 MHz, CDCl

3): δ 10.05 (s, 2H), 7.46(s, 2H), 3.97 (s, 6H).

Synthesis of compound (3): 2 (9.25 g, 40.9 mmol, 1 eq), allyl bromide (12.4 g, 102.25 mmol, 2.5 eq)

and K2CO3 (14.1 g, 102.25 mmol, 2.5 eq) were dissolved in DMF (90 mL). The mixture was stirred

overnight at 100 °C. The reaction mixture was poured in 250 mL water, after which it was extracted with ethyl acetate (3 x 200 mL). The organic layer was dried with MgSO4 and concentrated in vacuo,

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Figure E2. 1H-NMR of compound 3.

1H-NMR (400 MHz, CDCl

3): δ 7.40 (s, 2H), 6.04 (m, 2H), 5.48 (dq, J = 16, 2 Hz, 2H), 5.30 (dq, J = 16, 2

Hz, 2H), 4.59 (dt, J = 8, 2 Hz, 4H), 3.91 (s, 6H).

Synthesis of compound (4): A solution was made of THF, methanol and water (2:1:1), after which KOH

(6.1 g, 108.4 mmol, 4 eq) and 3 (8.3 g, 27.1 mmol, 1 eq) were added to the solution. The reaction mixture was stirred overnight for 5 nights at room temperature. Hereafter, the mixture was acidified using concentrated HCl, after which the mixture was concentrated in vacuo. The crude product was diluted with water (200 mL) and was extracted with ethyl acetate (3 x 200 mL). The organic layer was washed with brine and dried with MgSO4, after which it was filtered and the filtrate was

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Figure E3. 1H-NMR of compound 4.

1H-NMR (400 MHz, MeOH-d4): δ 7.46 (s, 2H), 6.06 (m, 2H), 5.49 (dq, J = 16, 2 Hz, 2H), 5.29 (dq, J = 16,

2 Hz, 2H), 4.64 (dt, J = 4, 2 Hz, 4H).

Synthesis of compound (5): 4 (1 g, 3.6 mmol, 1 eq), pentafluorophenol (1.7 g, 9 mmol, 2.5 eq), DIPEA

(2.42 mL, 14.4 mmol, 4 eq) and HBTU (4.1 g, 10.8 mmol, 3 eq) were added to dry THF (40 mL) under N2 atmosphere. The reaction mixture was stirred overnight at room temperature for 5 days, after

which the mixture was concentrated in vacuo. The mixture was flushed on a silica loaded column with dichloromethane: cyclohexane 1:1. The solution was concentrated in vacuo, which gave the crude product. The crude product was hereafter repeatedly washed with petroleum ether, while discarding the layer of petroleum ether until TLC (dichloromethane: cyclohexane 1:1) only showed two spots, after which the crude product was recrystallized from heptane, which yielded in 1.1 g of compound 5. (58% yield)

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Figure E4. 1H-NMR of compound 5.

1H-NMR (400 MHz, CDCl

3): δ 7.66 (s, 2H), 6.05 (m, 2H), 5.53–5.47 (dq, J = 16, 2 Hz, 2H), 5.34–5.31 (dq,

12, 2 Hz, 2H), 4.70 (dt, J = 8, 2 Hz, 4H).

Synthesis of compound (6): NaOH (10 g, 250 mmol, 1.6 eq) was dissolved in water (100 mL), after

which methoxy phenol (20 g, 161 mmol, 1 eq) was added slowly to the solution. Hereafter,

paraformaldehyde (17.4 g, 580 mmol, 3.6 eq) was added to the reaction mixture. The reaction was stirred overnight for 5 nights at room temperature, after which the mixture was acidified using concentrated HCl. The acidified mixture was chilled in a brine/ice bath. The precipitated solid was then filtrated and washed on the filter with water. Hereafter, the product was dried, which yielded in 27.42 g of compound 6. (93% yield)

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Figure E5. 1H-NMR of compound 6.

1H-NMR (400 MHz, CDCl

3): δ 7.58 (s, 1H), 6.66 (s, 2H), 4.80 (d, J = 8 Hz, 4H), 3.75 (s, 3H), 2.35 (t, J = 6

Hz, 2H).

Synthesis of compound (7): A 33% solution of HBr in acetic acid (7.4 mL, 40.8 mmol, 2.5 eq) was

added to glacial acetic acid (6 mL). The solution was cooled to approximately 10 °C, after which 6 (3 g, 16.2 mmol, 1 eq) was added. The product crashed out, causing a thick paste to be formed. The reaction mixture was kept at 15-20 °C for 2 hours and stirred by hand once every hour. The thick paste was then vacuum filtrated and washed on the filter with cold acetic acid and petroleum ether. The crude product was purified with column chromatography, using pure dichloromethane as eluent. The purified product was concentrated in vacuo, which yielded in 1.87 g of compound 7. (37% yield)

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Figure E6. 1H-NMR of compound 7.

1H-NMR (400 MHz, CDCl

3): δ 6.83 (s, 2H), 4.53 (s, 4H), 3.77 (s, 3H).

Synthesis of compound (8B): Dry THF (100 mL) was added to a dry round-bottom flask under N2

atmosphere. But-3-yn-1-ol (1.95 mL, 25.76 mmol, 8 eq) was added to the THF, after which a 60% dispersion of NaH (1.17 g, 28.98 mmol, 9 eq) was added slowly to the reaction mixture. After waiting for approximately 10 mins 7 (1 g, 3.22 mmol, 1 eq) was added slowly. The reaction mixture was stirred for 2 hours at room temperature, while monitoring the reaction using TLC (petroleum ether: ethyl acetate, 5:1). After the reaction was completed, the mixture extracted with ethyl acetate (200 mL) and a saturated solution of NH4Cl in water (100 mL). The aqueous layer was extracted with ethyl

acetate (2 x 100 mL), after which the organic layers were combined and dried with MgSO4. The

mixture was filtered and concentrated in vacuo. Hereafter, the crude product was purified with column chromatography, using the eluent that was used for the TLC. The purified product was concentrated in vacuo, which yielded in 0.23 g of 8B. (23% yield)

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Figure E7. 1H-NMR of compound 8B.

1H-NMR (400 MHz, CDCl

3): δ 7.15 (s, 1H), 6.73 (s, 2H), 4.65 (s, 4H), 3.75 (s, 3H), 3.66 (t, J = 6 Hz, 4H),

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Figure E8. 13C-NMR of compound 8B.

13C-NMR (100 MHz, CDCl

3): δ 152.9, 147.8, 124.7, 113.7, 81.2, 70.1, 69.8, 68.6, 55.9, 20.0.

Synthesis of compound (9B): Dry acetonitrile (3 mL), 4Å molecular sieves (0.15 g), Cs2CO3 (0.2 g, 0.6

mmol, 4 eq) and 8B (0.1 g, 0.31 mmol, 2.1 eq) were added to a dry flask under N2 atmosphere. 5

(0.08 g, 0.15 mmol, 1 eq) was added to the mixture, after which the reaction was stirred overnight for 5 nights at 50 °C. After 5 nights, the mixture was filtered over celite, after which the solution was concentrated in vacuo. Column chromatography (dichloromethane + 0.5% methanol) was used to purify the crude product, which yielded in 0.10 g of 9B. (81% yield)

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Figure E9. 1H-NMR of compound 9B.

1H-NMR (400 MHz, CDCl

3): δ 7.63 (s, 2H), 7.01 (s, 4H), 6.08 (m, 2H), 5.49 (dq, J = 16, 2 Hz, 2H), 5.30

(dq, 12, 2 Hz, 2H), 4.70 (dt, J = 8, 2 Hz, 4H), 4.54 (s, 8H), 3.85 (s, 6H), 3.55 (t, J = 6 Hz, 8H), 2.45 (dt, J = 4 Hz, 8H), 1.96 (t, J = 4 Hz, 4H).

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Figure E10. 13C-NMR of compound 9B.

13C-NMR (100 MHz, CDCl

3): δ 164.0, 157.8, 151.8, 140.2, 132.6, 132.0, 124.3, 118.5, 117.1, 113.9,

81.4, 70.6, 69.5, 68.4, 68.2, 55.8, 19.9.

Synthesis of compound (10B): Dry 1,4-dioxane (2 mL), 9B (120 mg, 0.15 mmol, 1 eq), diethylamine (44

mg, 0.60 mmol, 4 eq) and Pd(PPh3)4 (9 mg, 0.0075 mmol, 0.05 eq) were added to a dry flask under N2

atmosphere. The reaction mixture was stirred overnight at room temperature. Hereafter, the mixture was diluted with ethyl acetate (6 mL) and a 1M solution of HCl in water (3 mL), after which the mixture was extracted with brine (3mL) and the organic layer was dried with MgSO4. The

resulting mixture was filtrated and concentrated in vacuo, after which column chromatography (dichloromethane + 2% ethyl acetate) was used to purify the crude product, which after concentrating in vacuo yielded in 59 mg of 10B. (53% yield)

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Figure E11. 1H-NMR of compound 10B.

1H-NMR (400 MHz, CDCl

3): δ 9.83 (s, 2H), 7.80 (s, 2H), 7.01 (s, 4H), 4.49 (s, 8H), 3.85 (s, 6H), 3.55 (t, J

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Figure E12. 13C-NMR of compound 10B.

13C-NMR (100 MHz, CDCl

3): δ 167.8, 158.0, 153.5, 139.5, 131.8, 118.5, 118.2, 114.2, 81.1, 69.5, 68.5,

68.2, 55.7, 19.8.

Synthesis of compound (11B): 10B (53 mg, 0.07 mmol, 1 eq) dissolved in 20 mL dry THF, TMEDA

(0.003 mL, 0.024 mmol, 0.38 eq) dissolved in 1 mL dry THF and CuCl (2.4 mg, 0.024 mmol, 0.38 eq) were added in sequence to a dry flask under N2 atmosphere. The reaction mixture was stirred

overnight at room temperature, after which it was concentrated in vacuo. The concentrate was diluted in water (20 mL) and was extracted with ethyl acetate (3 x 25 mL), the organic layer was hereafter dried with MgSO4, filtrated and concentrated in vacuo. A TLC (DCM + 2% ethyl acetate) was

taken of the concentrate, which only showed the spot of the starting material. A 1H-NMR was also

taken of the concentrate and no product peaks were observed. (0% yield and 0% conversion)

Synthesis of compound (17B): 9B (40 mg, 0.05 mmol, 1 eq) dissolved in 15 mL dry THF, TMEDA

(0.0015 mL, 0.01 mmol, 0.2 eq) dissolved in 1 mL dry THF and CuCl (1 mg, 0.01 mmol, 0.2 eq) were added in sequence to a dry flask under N2 atmosphere. The reaction mixture was stirred overnight at

room temperature, after which it was concentrated in vacuo. The concentrate was diluted in water (20 mL) and was extracted with ethyl acetate (3 x 25 mL), the organic layer was hereafter dried with MgSO4, filtrated and concentrated in vacuo. A 1H-NMR of the crude mixture was taken, which

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(2) Huber, G. W.; Shabaker, J. W.; Dumesic, J. A. Science 2003, 300 (5628), 2075–2077. (3) Dunn, B.; Kamath, H.; Tarascon, J.-M. Science 2011, 334 (6058), 928–935.

(4) Wertz, S.; Studer, A. Green Chem. 2013, 15 (11), 3116–3134. (5) Melone, L.; Punta, C. Beilstein J Org Chem 2013, 9, 1296–1310.

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