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28th June 2012 @ 06:16
The alpha proton on the thiophene ring of the thienopyrimidine core has not succesfully been deprotonated by butyllithium reagents. Protection of the free amine should enable this deprotonation to take place by masking the interfering amine. A benzyl protecting group - which can withstand butyllithiums - is to be used for this purpose.

Conclusion: Starting materials were recovered from this reaction. These reaction conditions are not strong enough to drive benzylation.

2548.png


Experiment start time: 3:00 pm, 28/06/2012

Thieno[3,2-d]pyrimidin-4-amine (200 mg, 1.32 mmol, 1 equiv.) was dissolved in acetonitrile (10 mL) and stirred at rt under nitrogen. Triethylamine (0.4 mL, 2.8 mmol, 2 equiv.) was added dropwise. Condensation appeared on the side of the reaction vessel. To this stirring solution was added benzyl bromide dropwise (0.34 mL, 2.8 mmol, 2 equiv.). This solution was stirred at rt for 25 hr. TLC (photograph not taken) shows three new materials alongside significant amounts of benzyl bromide. (spot at rf=1 (not UV active, stains red with vanillin) spot at rf=0.45 uv active does not stain with vanillin. spot at rf=0.1, uv active and stains red with vanillin). At +25 hr the reaction was extracted with ethyl acetate (40 mL) and the organic layer was washed with water (3 x 30 mL) and brine (30 mL) before being dried over anhydrous magnesium sulfate. The solvents were removed and the product dried to yield a pale yellow solid (42.4 mg).

Expectation: Products are SM, BnBr, TEA, mono-substituted benzyl-SM and di-substituted benzyl-SM.

This solid was purified using flash chromatography, whereby the aforementioned solid was dry loaded onto the column, with the remnants that were not dry loaded dissolved in DCM and loaded on in the standard manner. The products were eluted using 5% EtOAc/hexane, increasing to 10% EtOAc/hexane, then 20% EtOAc/hexane. Two products were eluted using this (relatively) non-polar solvent system. Polarity was increased to 1% MeOH/DCM, which was increased first to 5% MeOH/DCM, followed by 10% MeOH/DCM. Three products were eluted using these polar solvent systems. TLC analysis of the column indicated that each product was separated in a pure fashion. The products eluted are as follows:

Fraction 1 (c3-c8 [5% EtOAc/hexane]): 11.1 mg
NMR:
1.zip
JRC19-1F1.pdf

Fraction contains benzyl bromide

Fraction 2 (c10-c15 [10% EtOAc/hexane]): 0 mg
Fraction 3 (c56-c64 [1% MeOH/DCM]): 1.1 mg
NMR:
3.zip
JRC 19-1 F3.pdf

Fraction contains peaks consistent with neither SM or BnBr

Fraction 4 (c67-c72 [10% MeOH/DCM]): 0.5 mg
Fraction 5 (c73-c95 [10% MeOH/DCM]): 4 mg
NMR:
5.zip
JRC 19-1 F5.pdf


(Note: Next time use 5% EtOAc/hexane increasing to 10%, and expect products for both. Then use 1% MeOH/DCM and expect one product. Then use 10% MeOH/DCM and expect two distinct products.)

Starting materials were isolated from this column, albeit in terrible yield (even though the column was done well, for once).
Attached Files
28th June 2012 @ 02:53
A deuterium oxide quench of JRC 17-1 in the presence of sec-butyllithium (JRC 16-8) showed a complex 1H-NMR spectrum which I haven't yet fully interpreted. Nevertheless, since something happened, there is hope. This experiment is designed to see if I can iodonate the 5 position on the thiophene ring, based off the assumption that the something that happened in JRC 16-8 was the removal of the desired proton.

Conclusion: The desired product was formed in 4% yield. This low yield is probably a reflection upon the column used.

2536.png


Reaction start time: 11:00 am, 28/06/2012
4-(Thieno[3,2-d]pyrimidin-4-yl)morpholine (105 mg, 0.47 mmol, 1 equiv.) was dissolved in dried THF (4 mL) and stirred under argon at -78 °C for 10 min. sec-Butyllithium solution (1.4 M, 0.34 mL, 0.48 mmol, 1 equiv.) was added at this temperature dropwise. The stirring solution turned a bright orange colour upon addition of the butyllithium reagent. The stirring solution was allowed to warm to -40 °C, and the stirring solution was maintained at this temperature for 1 hr. The stirring solution was cooled to -78 °C and a solution of elemental iodine (120.9 mg, 0.476 mmol, 1 equiv.) in dried THF (3 mL) and added dropwise to the stirring reaction solution. TLC at + 4.5 hr indicates the presence of new material, as well as some starting material remaining.

TLC at +4.5 hr (10% MeOH/DCM): visualised with UV/potassium permanganate
JRC 18-1 (3pm 28th).JPG


The balloon at this time was replaced with another containing argon, to be maintained overnight. TLC at +25 hr indicates formation of 3 new products.

TLC +25 hr (10% MeOH/DCM) Visualised with UV/vanillin:
TLC plate not photographed (camera was dead). One new spot (UV active) on baseline. One new spot (UV active) at rf = 0.3. One new spot (UV active, stained yellow with vanillin) at rf = 0.5.

At +27 hr the reaction was quenched by the addition of water (5 mL), with no visible signs of reaction. The reaction was moved to regular atmosphere and extracted with DCM (20 mL). The organic layer was washed with sodium thiosulfate until the solution remained a pale yellow colour. The organic layer was then washed with water (3 x 20 mL) and brine (40 mL) before being dried over anhydrous magnesium sulfate. The solvents were removed and the product dried in vacuo to yield a bright yellow solid (85.5 mg). 1H-NMR indicates a mixture of at least two products.

1H-NMR:
2.zip
JRC18-1(2).pdf


Low Res. Mass Spec:
Want: 347. Found: 278.
This is consistent with the structure of the compound I was trying to make in JRC 16-1: 6-iodothieno[3,2-d]pyrimidin-4-amine.

The product was purified by column chromatography. 40% EtOAc/hexane was used first, and after the first product eluted the solvent system polarity was increased using 10% MeOH/DCM. Two fractions were collected:

Fraction 1: 7 mg (4%)
Fraction 2: 85.1 mg

The column did not give great separation. Some of fraction 1 was lost on the column and/or eluted with fraction 2. 1H-NMR indicated that fraction 1 contained the desired compound.

1H-NMR:
f1.zip
JRC18-1F1.pdf


1H-NMR indicated that fraction 2 contained the desired compound with traces of other material.

1H-NMR:
f2.zip
JRC18-1f2.pdf


The presence of the morpholine signals in these spectra indicates that the product observed in the low res. mass spec. probably underwent degeneration in the mass spec. machine.
Attached Files
27th June 2012 @ 03:40
Previous experiments in the JRC 16-x series have failed to remove the desired proton from the thiophene ring. This experiment is designed with the exploration of different synthetic pathways in mind. If this reaction leads to the abstraction of the desired proton it represents another synthetic possibility towards the thienopyrimidine target.

Reaction start time: 11:40 am, 27/06/2012
Thieno[3,2-d]pyrimidine-4(3H)-one (51.8 mg, 0.34 mmol, 1 equiv.) was dissolved in THF (5 mL) with sonification and heating (formed cloudy, white solution). This solution was stirred at -78 °C under argon before sec-butyllithium solution was added dropwise (1.4 M, 0.51 mL, 0.71 mmol, 2 equiv.). Solution seemed to remain pale and whhite. The stirring solution was then allowed to warm to -40 °C. The stirring solution was maintained at this temperature for 1 hr before deuterium oxide (0.6 mL, 33.3 mmol, 97 equiv.) was added. The solution was then allowed to warm to rt before being extracted with diethyl ether (5 mL). The organic layer was dried over anhydrous magnesium sulfate before the solvent was removed and the product dried in vacuo to yield a white film (4 mg).

1H-NMR:

Risk Assessment: As for JRC 16-2
Attached Files
27th June 2012 @ 03:38
This experiment, in the JRC 16-x series, aims to determine if the morpholine derivative can be deprotonated using sec-BuLi.

Conclusion: A proton on the thiophene ring has likely been deprotonated. NMR is consistent with this conclusion. More investigation is needed to fully characterise the extent of this deprotonation.

2712.png


Reaction start time: 11:40 am, 27/06/2012

4-(Thieno[3,2-d]pyrimidin-4-yl)morpholine (48.7 mg, 0.22 mmol, 1 equiv.) was dissolved (easily) in THF (5 mL). This solution was then cooled to -78 °C before sec-butyllithium was added dropwise (1.4 M, 0.17 mL, 0.24 mmol, 1.1 equiv.), at which time the solution began turning dark orange. The stirring solution was allowed to warm to -40 °C, and the stirring solution was maintained at this temperature for 1 hr, after which time deuterium oxide (0.6 mL, 33.3 mmol, 134 equiv.) was added dropwise. The solution was allowed to warm to rt before being extracted with diethyl ether (4 mL). The organic layer was dried over anhydrous magnesium sulfate, and the solvent removed and product dried in vacuo to yield a bright yellow solid (11 mg).

1H-NMR:
1.zip
JRC16-8.pdf


The spectrum indicates the presence of starting material, alongside two new products. The numbers of peaks present is consistent with starting material (2 x doublet, 1 x singlet), starting material with altered shift (2 x doublet, 1 x singlet), a broad amine peak, and new material (2 x singlet). This accounts for all peaks. This provides the best evidence yet of a succesful deprotonation.

TLC of product shows one spot (rf = 0.45 in 10% MeOH/DCM).
Attached Files
27th June 2012 @ 03:36
JRC 16-6 failed to show the desired proton being removed, though the 1H-NMR either indicated that a number of protons had been removed, or that the spectrum was poorly shimmed. In any case, this experiment is a repeat of that previous effort, using even more sec-BuLi than last time, so that a conclusion for this series of experiments might be reached.


Reaction start time: 12:15, 27/06/2012
Thieno[3,2-d]pyrimidin-4-amine (50.0 mg, 0.33 mmol, 1 equiv.) was dissolved in THF (8 mL) with sonification and heating. The solid did not dissolve well, though it was mostly dissolved after approx. 1 min sonification and boiling). The solution was stirred under argon at -78 °C before sec-butyllithium solution (1.4 M, 2.10 mL, 2.94 mmol, 8.9 equiv.) was added dropwise. The solution turned from pale orange to a dark orange colour as the addition progressed. Once addition was complete the reaction mixture was stirred for 10 min before being allowed to warm to -15 °C. The reaction mixture was maintained at this temperature with stirring for 1 hr. The mixture was then quenched by the addition of deuterium oxide (1.0 mL, 55 mmol, 18.7 equiv.), and the reaction mixture extracted with diethyl ether (3 mL). The organic layer was dried over anhydrous magnesium sulfate before the solvent was removed and the product dried in vacuo to yield a granular yellow solid (21.7 mg).

TLC shows two spots: One on the baseline, and one at rf = 0.45 (10% MeOH/DCm). TLC plate lost in permanganate visualiser.

1H-NMR:
1.zip
JRC16-7.pdf
Attached Files