Bachelor Thesis Scheikunde
Fe-catalyzed carbene transfer to isocyanides in the
synthesis of 6-amino-4-pyrimidones
Employment of varying methods for the synthesis of isocyanides and
alpha-diazo esters
by
Matthijs Justin Boel
16-Maart-2021
Studentnummer
UvA: 12000566, VU: 2610944
Onderzoeksinstituut
Verantwoordelijk docent
FNWI
dr. E. Ruijter
Onderzoeksgroep
Begeleider
Synthetic and Bio-Organic Chemistry
Daniël H. Preschel & Thomas R.
Roose
Samenvatting
Cyanide, een driedubbele binding tussen een koolstof- en stikstofatoom, is redelijk bekend buiten de chemie voor zijn giftigheid, waar het ook werd gebruikt als pil voor spionnen rond de koude oorlog. Binnen de organische chemie wordt de cyanide vooral als functionele groep gebruikt. Als de cyanide groep in de chemie bekend staat voor zijn giftigheid dan staat zijn structurele weerspiegeling, de isocyanide, bekend voor zijn doordringende stank. Ten opzichte van de cyanide groep zit de isocyanide groep verbonden aan het molecuul via het stikstofatoom in plaats van het koolstofatoom, wat het een interessante reactiviteit geeft. Het koolstofatoom is in het begin nucleofiel en valt snel een ander molecuul aan, maar dit maakt het koolstofatoom juist elektrofiel, waardoor het aangevallen kan worden door een ander molecuul.
Deze reactiviteit kan gebruikt worden in de organometaalchemie bij de zogenaamde carbeen transfer reactie. Hierbij wordt een diazo verbinding door een transitiemetaal omgezet tot een carbeen, een neutrale koolstof die een valentie van twee heeft, en kan daarna reageren met een isocyanide om een ketenimine te vormen. Dit ketenimine heeft twee elektrofiele atomen en is redelijk reactief. In dit geval kan een amidine, een molecuul met twee nucleofiele stikstofatomen, gebruikt worden om uiteindelijk een 6-amino-4-pyrimidon te vormen. Dit soort reacties worden ook wel Multi-Component Reactions (MCRs) genoemd omdat er meer dan twee aparte moleculen met elkaar reageren om een product te vormen. Tot nu toe is de carbeen transfer reactie succesvol uitgevoerd met een palladium katalyst, maar recent is er gekeken naar de ijzer katalysator TBA[Fe], dit omdat ijzer veel vaker voorkomt en ook goedkoper is dan een edel metaal als palladium. Tot nu toe werkt de MCR met de TBA[Fe] gekatalyseerde carbeen transfer reactie goed maar de scope van de reactie moet nog verder onderzocht worden, dit kan vooral gedaan worden door meerdere varianten van de isocyanide en diazo componenten te synthetiseren voor gebruik in testreacties. In dit artikel worden meerdere methodes gebruikt om verschillende isocyanides en alpha-diazo esters te synthetiseren en worden een paar isocyanides ingezet in de MCR. Er wordt met name gekeken naar mogelijke toepassingen van de 6-amino-4-pyrimidonen die daarbij gevormd kunnen worden.
1
Abstract
Isocyanides are a versatile building block for the synthesis of organic molecules. This is due to their unique polar structure making them an electrophile as well as nucleophile. The isocyanide building block can be used for a multitude of useful applications. One of these useful application for isocyanides is within the field of Multi Component Reactions (MCR). The reaction that’s focused on in this thesis is an Isocyanide Multi Component Reaction (IMCR) involving an isocyanide, an alpha-diazo ester as well as an amidine reacting together with a metal catalyst to form 6-amino-4-pyrimidones, which are precursors for some medical compounds. More specifically, the MCR involves a carbene transfer between the isocyanide and the alpha-diazo compounds using the catalyst, afterwards the amidine performs two nucleophilic attacks to close the ring.
Up until recently a palladium catalyst has been used for the carbene transfer portion of the IMCR, this catalyst has shown to be effective with a large scope but is also expensive. In the past few years however there’s been a focus on an iron based catalyst, namely the TBA[Fe] catalyst. So far the scope of the IMCR using this catalyst for the carbene transfer has been explored through the use of isocyanide and amidine derivatives. Alpha-diazo ester derivatives have not been explored as much as of yet, and could give more insight into what the iron catalyst structurally allows for. For further exploration of the IMCR as well as potential IMCR and post-IMCR modifications several isocyanide and alpha-diazo ester derivatives were synthesised.
In this thesis two different pathways for isocyanide synthesis were used to synthesise more unique isocyanides to further test the IMCR’s scope. The traditional formamide dehydration pathway has been regularly employed in the synthesis of numerous isocyanides and was used here as well. The second pathway used in this thesis is a novel synthesis method by Zhang et al. which turns an amine into an isocyanide group in a one-step reaction using a difluorocarbene. A ribose based isocyanide synthesis was also attempted through the use of a novel Leuckart-Wallach reductive amination approach by Dömling et al. which has successfully been employed on several pyranoses. The alpha-diazo esters were synthesised using a novel sulfonyl-azide-free (SAFE) approach by Krasavin et al. Lastly, the IMCR was tested with some of the synthesised isocyanides.
2
List of Abbreviations
Ac Acetate Bn Benzyl C-hex Cyclohexane DBU Diazabicycloundecene DCM Dichloromethane DMF Dimethylformamide El Electrophile Et EthylHRMS High-Resolution Mass Spectrometry
IR Infrared spectroscopy
IMCR Isocyanide Multi Component Reaction
MCR Multi Component Reaction
Me Methyl
MeOH Methanol
NMR Nuclear Magnetic Resonance
Nu Nucleophile
Ph Phenyl
rt room temperature
TBA Tetrabutylammonium
TBAHS Tetrabutylammonium hydrogensulfate
TBOK Potassium t-Butyloxide
THF Tetrahydrofuran
TLC Thin Layer Chromatography
3
Table of Contents
1. Introduction……….4
1.1 Isocyanides in Organic Chemistry……….4
1.2 The Carbene Transfer Reaction………....4
1.3 Isocyanide Synthesis Methods………..6
1.4 Alpha-diazo Ester Synthesis Method………6
2. Experimental Section and Results……….7
2.1 Materials………..7
2.2 Isocyanide Synthesis……….8
2.2.1 Formamide Dehydration Method………...8
2.2.2 Zhang Difluorocarbene Method……….9
2.2.3 Ribose Isocyanide Leuckart-Wallach Method………10
2.2.4 Ribose Isocyanide Standard Approach General Tosylation Method………..10
2.2.5 Ribose Isocyanide Standard Approach Furanose-Specific Tosylation Method…10 2.3 Krasavin SAFE Alpha-diazo Ester Synthesis Method……….10
2.4 TBA[Fe] Catalysed IMCR………11
2.4.1 TBA[Fe] Catalysed 6-Amino-4-pyrimidone Method………..11
2.4.2 TBA[Fe] Catalysed Methyl-2-isocyanobenzoate Method……….11
3. Discussion……….11
3.1 Isocyanide Synthesis………..11
3.2 Alpha-diazo Ester Synthesis………..13
3.3 Carbene Transfer Reactions………..13
3.4 Potential Future Applications……….14
4. Conclusion………14
5. Acknowledgments………..15
4
1. Introduction
1.1 Isocyanides in Organic Chemistry
The cyanide functional group is one of the few chemistry related subjects that has made its way out of its scientific field and into the minds of the general populace, mainly due to its usage in media such as movies as a highly toxic compound. And while the toxic nature of molecules containing the moiety is equally well known in the scientific community its usefulness as a versatile C1 building block in organic chemistry is of importance as well. In this thesis, however, the cyanide group’s isomeric counterpart, the isocyanide group, is focused on. If the cyanide group is most well-known for its toxicity then the isocyanide group is known for its volatile nature and unpleasant, strong odour.1 In comparison to the cyanide group, with its
triple bonded carbon and nitrogen atoms, the isocyanide moiety is attached to the rest of the molecule through the nitrogen atom. This difference in connectivity results in a unique situation where a single carbon atom is attached to the molecule through a heteroatom while remaining stable, which gives this group an interesting resonance structure
that’s between a zwitterionic and carbene form (Scheme 1).2 This
arrangement gives the carbon atom a unique property, at first the carbon atom has a nucleophilic nature, yet the carbon atom in structure 2.2 that is formed after a nucleophilic attack has an electrophilic nature, allowing another nucleophile, inter- or intramolecular, to attack, yielding the imine 2.3 (Scheme 2). This
unique reactivity is one of the reasons isocyanides are often used in organic chemistry. Furthermore, the isocyanide group is isoelectronic with the carbonyl ligand, which readily coordinates with metal complexes (Scheme 1).3 The isocyanide moiety’s ability to interact with
metal complexes allows for it to be applied in the field of organometallic chemistry as well.
Isocyanides are often used in the synthesis of numerous diverse synthetic scaffolds. Their most prominent use is in Multi Component Reactions (MCRs) where the typical reactivity of the isocyanide plays a key role. A prominent example is the well-known isocyanide based MCR (IMCR) Ugi-4CR (Scheme 3).4
1.2 The Carbene Transfer Reaction
One such IMCR that this thesis focuses on involves the transition metal catalysed carbene transfer reaction with an isocyanide and an alpha-diazo ester compound as its reagents. This reaction has traditionally been employed with Palladium, as well as Rhodium.5
In this catalytic cycle the carbene is generated as the alpha-diazo ester coordinates with the metal complex to form the metallocarbene 4.1, which causes the elimination of nitrogen gas,
Scheme 2: Typical reactivity of isocyanide moiety
Scheme 3: Ugi-4CR reaction
Scheme 1: Resonance of isocyanide and carbonyl
5 after which a migratory insertion of the isocyanide, also coordinated to the metal complex, occurs to form the ketenimine 4.3 (Scheme 4).
More recently interest has shifted towards base metal catalysed versions of these reactions, due to their relative abundance and cheaper costs compared to rare earth metals like palladium. In recent years an iron catalysed version of the formation of the metallo-carbene complex from an alpha-diazo ester has been performed.6 The iron complex used in this is the
TBA[Fe] catalyst, also refered to as the Hieber anion with an iron (II-) centre and Tetrabutylammonium as its counterion (Figure 1).7 Our research group
has successfully applied the TBA[Fe] catalyst in the formation of ketenimines through the carbene transfer to isocyanides. The resulting ketenimine
intermediate has two electrophilic centers which can readily be reacted with nucleophilic compounds. Our group has come up with a procedure where the ketenimine 5.1 reacts with a bisnucleophilic compound, amidines in this case, to yield compounds 5.3, known as 6-amino-4-pyrimidones (Scheme 5). These pyrimidones act as precursors to multiple natural and medicinal products, such as the anticancer drug Dasatanib (Figure 2).
To further illustrate the effectiveness of the TBA[Fe] catalyst in this transformation the scope needs to be explored further. In order to broaden the scope of this reaction several custom isocyanides and diazo esters will be synthesised. The focus will be on the isocyanide and alpha-diazo ester scope.
Scheme 4: Carbene transfer isocyanide insertion catalytic cycle. M = Pd, Rh
Scheme 5: TBA[Fe] catalysed 6-amino-4-pyrimidone MCR mechanism
Figure 2: Structure of Dasatanib
Figure 1: Hieber anion structure
6 Scheme 7: Proposed mechanism by Zhang et al. for the difluorocarbene method
1.3 Isocyanide Synthesis Methods
The traditional, most often used synthesis pathway for isocyanides is the formamide dehydration method used by Ugi et al. (Scheme 6.1)1 This two-step procedure
involves the dehydration of a formamide (b) with a dehydrating agent such as phosphoryl oxychloride to form an isocyanide (c). In this thesis the formamide is formed from an amine (a), which reacts with the mixed acetic formic anhydride (1). However, recently a new approach has been formulated by Zhang et al. (Scheme 6.2).8 This is a one-step method
which uses a difluorocarbene as building block.
The authors propose that the mechanism starts with the activation of the difluorocarbene 7.2, which occurs through the decarboxylation of sodium 2-chlorodifluoroacetate (7.1) in the presence of a base (Scheme 7). The difluorocarbene is attacked by the amine to form complex 7.3, after which a process similar to the dehydration step in the formamide method occurs through the double elimination of hydrogenfluoride, which then results in the formation of the isocyanide. These two methods will be employed to synthesise the isocyanides. Unlike the isocyanides, the alpha-diazo esters will be synthesised using a single method.
1.4 Alpha-diazo Ester Synthesis Method
The synthesis of alpha-diazo esters usually occurs through the diazo transfer reaction with active methylene groups as originally formulated by Regitz et al.9 Recently a one-step
sulfonyl-azide-free (SAFE) method has been published by Krasavin et al., which uses m-carboxybenzenesulfonyl azide generated in situ from sodium azide and m-carboxybenzenesulfonyl chloride as the transfer reagent (Scheme 8).10
Scheme 8: The SAFE diazo transfer reaction
7 For the planned alpha-diazo esters the required methylene precursor protons aren’t acidic enough for a viable azide transfer reaction. As such a variant of the Danheiser deacylative diazo transfer will be used for the synthesis of these alpha-diazoesters, which requires slightly modified variants of the methylene precursor (Scheme 9).11 The more acidic
methylene group, which has one of its protons substituted with an acetyl group in the Danheiser variant, is first deprotonated by a base. The resulting stabilised carbanion 9.1 is then attacked by the in situ generated transfer reagent to form unstable intermediate 9.2 which rearranges to 9.3, after which a sulfonyl acetamide is eliminated to yield the diazo compound. The isocyanides and alpha-diazo esters that are planned to be synthesised are shown in figure 4. If possible, some of the isocyanides will be used in test-reactions for the TBA[Fe] catalysed 6-amino-4-pyrimidone IMCR.
2. Experimental Section and Results
2.1 Materials
All purchased solvents and reagents were used without further purification. Anhydrous THF, DCM and DMF were collected from an Inert Solvent Purification system. NMR spectra were determined with a Bruker Avance 500 or Bruker Avance 300 with residual chloroform solvent used as IS (1H: δ 7.26 ppm, 13C {1H}: δ 77.16 ppm). Chemical shifts are reported in
ppm. Couplings are indicated with, or combinations of s (singlet), br (broad singlet), d (doublet), t (triplet), q (quartet) and multiplet (m) and coupling constants (J) are reported in Hertz. Silicycle Silia-P Flash Silica Gel (40-63 μm particle size, 60Å pore diameter) was used for flash chromatography along with specified eluents. TLC plates from Merck (SiO2, Kieselgel 60 F254 neutral, on aluminium with fluorescence indicator) were used to perform TLC and stains were visualized with 254 nm UV detection. For masses Electrospray Ionization (ESI) high-resolution mass spectrometry (HRMS) was carried out using a Bruker microTOF-Q instrument in positive ion mode (capillary potential of 4500 V). IR was determined neat with a Shimadzu FTIR-8400s
Scheme 9: Proposed mechanism of the deacylative Danheiser variant of the SAFE diazo transfer
8 spectrophotometer with wavelengths noted in cm-1. Melting point (m.p.) was measured with a
Stuart SMP50 Automatic Digital Melting Point apparatus.
2.2 Isocyanide Synthesis
2.2.1 Formamide Dehydration Method:
o-Iodophenyl isocyanide: Formic acid (0.76 mL, 20.0 mmol, 1.0 eq.) and acetic
anhydride (1.89 mL, 20.0 mmol, 1.0 eq.) were heated at 65 °C and mixed for 2 hours to form the mixed anhydride 1 without further purification. To a solution of o-iodo aniline (4.38 g, 20.0 mmol, 1.0 eq.) in CH2Cl2 (40 mL) was added the crude of mixed anhydride 1 (1.76 g, 20 mmol,
1 eq.) dropwise in an ice bath and stirred for 2 hours (Scheme 6.1). The acetic acid was then evaporated and the crude was evaporated with toluene twice and dried under vacuum.
Triethylamine (16.73 mL) was added to a solution of the o-iodophenyl formamide in CH2Cl2 (125.6 mL, 120 mmol, 6.0 eq.) at 0°C in a dried and flushed Schlenk. POCl3 (3.73 mL,
40.0 mmol, 2.0 eq.) was added dropwise over a period of 10 minutes and the mixture was stirred for 2 hours and quenched with Na2CO3 (40.0 mL) for 30 minutes. The crude was
transferred to a separatory funnel and diluted with CH2Cl2 (200 mL). The organic layer was
then washed with half-saturated aqueous Na2CO3 (100 mL) and brine (100 mL) and
subsequently dried with Na2SO4, filtered and concentrated in vacuo. The resulting residue was
purified with recrystallization in n-hexane.
9-Isocyano fluorene: The starting material 9-aminofluorene hydrochloride (5 g, 23
mmol, 1.0 eq.) in CH2Cl2 (50.0 mL) was first deprotonated with saturated NaHCO3 (50.0 mL)
in a separatory funnel and the water layer was washed with CH2Cl2 (5 x 50.0 mL). The organic
fractions were collected and evaporated.
Formic acid (1.74 mL, 46.0 mmol, 2.0 eq.) and acetic anhydride (4.35 mL, 46.0 mmol, 2.0 eq.) were heated at 65°C and mixed for 2 hours to form the mixed anhydride 1 without further purification. To a solution of primary amine 9-aminofluorene (3.90 g, 21.5 mmol, 1.0 eq.) in CH2Cl2 (66.15 mL) was added the crude of mixed anhydride 1 (2.0 eq.) dropwise at 0°C and
stirred for 2 hours (Scheme 6.1). The acetic acid was then evaporated. The residue was then dissolved in toluene (50 mL) and the toluene evaporated twice and dried under vacuum.
Triethylamine (17.98 mL, 129.0 mmol, 6.0 eq.) was added to a solution of the fluoren-9-yl formamide in THF (135 mL) at -78°C in a dried and flushed Schlenk. POCl3 (4.01 mL, 43
mmol, 2.0 eq.) was added dropwise over a period of 10 minutes. The mixture was then slowly brought back up to room temperature over 2 hours and stirred for another hour. The mixture was quenched with a saturated aqueous solution of Na2CO3 (40.0 mL) for half an hour. The
crude was transferred to a separatory funnel and washed with diethyl ether (3 x 50.0 mL) followed by CH2Cl2 (50.0 mL). The solvent was evaporated under vacuum. The resulting
residue was purified with flash chromatography (14:1→8:1 c-hex/EtOAc).
Methyl-2-isocyanobenzoate: Formic acid (1.509 mL, 40.0 mmol, 2.0 eq.) and acetic
anhydride (3.78 mL, 40.0 mmol, 2.0 eq.) were heated at 65 °C and mixed for 2 hours to form the mixed anhydride 1 without further purification. To a solution of methyl anthranilate (1.8 mL, 13.8 mmol, 1.0 eq.) in CH2Cl2 (61.5 mL) was added the crude of mixed anhydride 1 (2.0 eq.)
dropwise in an ice bath and stirred for 2 hours (Scheme 6.1). The acetic acid was then evaporated. The crude was then dissolved in toluene (50 mL) and the toluene evaporated and dried under vacuum.
Triethylamine (6.94 mL, 49.8 mmol, 4.0 eq.) was added to a solution of the methyl-2-formamide benzoate in THF (50.0 mL) at 0°C in a dried and flushed Schlenk. POCl3 (1.74 mL,
18.67 mmol, 1.5 eq.) was added dropwise over a period of 10 minutes and the mixture was stirred for 2 hours and quenched with ice cold water(100 mL) for 30 minutes. The crude was transferred to a separatory funnel and washed with diethyl ether (3 x 150 mL) followed by brine (150 mL). The organic layer was subsequently dried with Na2SO4, filtered and concentrated in
9
o-iodophenyl formamide:
The formamide 2b was synthesised from o-iodoaniline (4.38 g, 20.0 mmol) and mixed anhydride 1 (1 eq.) and yielded a mixture of two rotamers, major rotamer given (1:0.6), as a colourless solid (3.90 g, 89%). Rf = 0.4 (2:1 c-hex/EtOAc) 1H
NMR (500 MHz, CDCl3): δ 8.49 (s, 1H), 7.80 (d, J = 5.0 Hz, 1H), 7.77 (d, J = 6.0
Hz, 1H), 7.50 (s, 1H), 7.35 (q, J = 7.0 Hz, 1H), 6.94 (t, J = 8.0 Hz, 1H) ppm. 13C
NMR (500 MHz, CDCl3): δ 140.1, 139.1, 138.9, 129.8, 129.6, 127.2, 126.6, 126.2, 122.4, 119.3
ppm. This is consistent with the reference.12 Two signals are missing from the 13C spectrum.
o-iodophenyl isocyanide:
The isocyanide 2c was synthesised from 2b and yielded a light-green powder (155.2 mg, 3.4%). Rf = 0.6 (2:1 c-hex/EtOAc) 1H NMR (500 MHz, CDCl3): δ 7.90 (d, J = 8.0
Hz, 1H), 7.43-7.36 (m, 2H), 7.08-7.13 (m, 1H) ppm. 13C NMR (500 MHz, CDCl 3): δ
139.8, 130.6, 129.2, 127.8, 94.5 ppm. This is consistent with the reference.12 Two
signals are missing from the 13C spectrum.
fluoren-9-yl formamide:
The formamide 3b was synthesised from 9-amino fluorene (3.90 g, 21.5 mmol) and mixed anhydride 1 (2 eq.) and yielded a colourless solid (3.88 g, 86%). Rf = 0.86 (1:1 c-hex/EtOAc) 1H NMR (300 MHz, CDCl3): δ 8.53 (s, 1H),
7.71 (d, J = 9.0 Hz, 2H), 7.59 (d, J = 7.8 Hz, 2H), 7.42 (t, J = 7.8 Hz, 2H), 7.32 (d, J = 7.5 Hz, 2H), 6.32 (d, J = 9.0 Hz, 1H), 5.72 (br s, 1H) ppm. This is consistent with the reference.13
9-isocyano fluorene:
The isocyanide 3c was synthesised from 3b and yielded a red powder (1.76 g, 43%). Rf = 0.57 (5% MeOH in DCM) IR: 2139 cm-1. 1H NMR (500 MHz,
CDCl3): δ 7.71 (4H), 7.47 (2H), 7.40 (2H), 5.62 (s, 1H) ppm. 13C NMR (500
MHz, CDCl3): δ 157.89, 140.25, 139.63, 129.94, 128.41, 124.98, 120.47,
56.86 ppm. m.p. 45-90°C (decomp).
methyl-2-formamidobenzoate:
The formamide 4b was synthesised from methyl anthranilate (1.8 mL, 13.82 mmol) and mixed anhydride 1 (2 eq.) and yielded a mixture of two rotamers, major rotamer given (1:0.2), as a colourless solid (2.23 g, 90%). Rf = 0.67 (2:1
c-hex/EtOAc) 1H NMR (500 MHz, CDCl
3): δ 10.98 (s, 1H), 8.95 (d, J = 11.5
Hz, 1H), 8.70 (d, J = 9.0 Hz, 1H), 8.51 (d, J = 3.0 Hz, 1H), 8.04 (dd, J = 6.5 Hz, 1.5 Hz, 1H), 7.55 (td, J = 10.0 Hz, 1.65 Hz, 1H), 7.12 (m, 1H), 3.92 (s, 3H) ppm. 13C NMR
(500 MHz, CDCl3): δ 168.63, 159.64, 140.53, 134.81, 131.03, 123.32, 121.31, 115.29, 52.56
ppm. This is consistent with the reference.14
methyl-2-isocyanobenzoate:
The isocyanide 4c was synthesised from 4b and yielded a red liquid (1.77 g, 88%). Rf = 0.4 (9:1 c-hex/EtOAc) 1H NMR (500 MHz, CDCl3): δ 8.00 (dd, J =
8.5 Hz, 1.5 Hz, 1H), 7.56 (m, 1H), 7.47 (t, J = 8.5 Hz, 2H), 3.97 (s, 3H) ppm. This is consistent with the reference.15
2.2.2 Zhang Difluorocarbene Method:
o-iodo aniline (876.1 mg, 4.0 mmol, 1.0 eq.) was mixed with CF2ClCO2Na (1.22 g, 8.0
mmol, 2.0 eq.) and K2CO3 (1.11 g, 8.0 mmol, 2.0 eq.) and dissolved in DMF (50 mL) in a dried
and flushed Schlenk. The mixture was then stirred vigorously for 12 hours at 100°C and cooled to room temperature afterwards. The mixture was transferred to a separatory funnel, diluted with CH2Cl2 (250 mL) and washed with water (4 x 250 mL) followed by brine (250 mL), then
10 dried with MgSO4, filtered and concentrated in vacuo. The resulting residue was purified with
flash chromatography (3:1→1:1 c-hex/EtOAc). The same method was used with methyl anthranilate, p-trifluoromethyl aniline and 2-thiophenemethylamine as starting material.
2-(isocyanomethyl)thiophene:
The isocyanide 6c was synthesised from 2-thiophenenemethylamine (0.41 mL, 4.0 mmol) and sodium chlorodifluoroacetate (1.22 g, 8.0 mmol) and yielded a red liquid (292 mg, 59%). Rf = 0.5 (1:1 c-hex/EtOAc) 1H NMR (300 MHz, CDCl3): δ
7.22 (d, J = 6.0 Hz, 1H), 6.97 (s, 1H), 6.92 (t, J = 3.6 Hz, 1H), 4.62 (d, J = 6.0 Hz, 2H) ppm. This is consistent with the reference.16
2.2.3 Ribose Isocyanide Leuckart-Wallach Method:
Ribose derivative 7a (500.0 mg, 1.19 mmol, 1.0 eq.) was dissolved in formamide (2.4 mL, 59.5 mmol, 50.0 eq.) and formic acid (225 μL, 5.95 mmol, 5.0 eq.) and the mixture was refluxed for 3 hours at 100°C (Scheme 10). Afterwards the mixture was transferred to a separatory funnel, diluted with CH2Cl2 (54.0 mL), washed with water and subsequently dried
with MgSO4, filtered and concentrated in vacuo. The crude was purified with flash
chromatography (2% MeOH in CH2Cl2).
2.2.4 Ribose Isocyanide Standard Approach General Tosylation Method:
Ribose derivative 7a (500.0 mg, 1.19 mmol, 1.0 eq.) was dissolved in DCM (4.8 mL), and p-toluene sulfonyl chloride (343.2 mg, 1.8 mmol, 1.52 eq.) and pyridine (0.21 mL, 2.56 mmol, 2.15 eq.) were added slowly at 0°C (Scheme 10). The reaction mixture was stirred and slowly brought back to room temperature over the period of 3 hours. The mixture was diluted with diethyl ether (12.2 mL), washed with water (20.0 mL), saturated NaHCO3 (20.0 mL) and
brine (20.0 mL), dried with MgSO4, filtered and concentrated in vacuo.
2.2.5 Ribose Isocyanide Standard Approach Furanose-Specific Tosylation Method:
Ribose derivative 7a (500.0 mg, 1.19 mmol, 1.0 eq.) was dissolved in DCM (4.8 mL), then p-toluene sulfonyl chloride (317.6 mg, 1.67 mmol, 1.4 eq.), tetrabutylammonium hydrogensulfate (20.20 mg, 0.06 mmol, 0.05 eq.) and a 5% aqueous solution of NaOH (3.25 mL, 8.65 mmol, 7.3 eq.) were added slowly and the reaction mixture was stirred at room temperature for 15 hours (Scheme 10). The mixture was diluted with DCM (12.2 mL), washed with water (20 mL), dried with Na2SO4, filtered and concentrated in vacuo. The crude was
purified with flash chromatography (3:1 c-hex/EtOAc).
2.3 Krasavin SAFE Alpha-diazo Ester Synthesis Method:
NaN3 (1.17 g, 18.0 mmol, 2.0 eq.), K2CO3 (3.32 g, 24 mmol, 2.67 eq.) and
m-carboxybenzenesulfonyl chloride (2.65 g, 12.0 mmol, 1.33 eq.) were dissolved in water (24 mL). Dimethyl-2-acetylsuccinate (1.46 mL, 9.0 mmol, 1.0 eq.) was added dropwise and the mixture was stirred vigorously at room temperature for 2 hours. Afterwards the aqueous layer was transferred to a separatory funnel and washed with chloroform (2 x 50.0 mL). The organic layers were collected, dried with CaCl2, filtered and dried in vacuo. The same method was
used with diethyl-2-acetylpentanedioate as starting material.
dimethyl-2-diazosuccinate:
The diazo compound 8b was synthesised from dimethyl-2-acetylsuccinate (1.46 mL, 9.0 mmol) and sodium azide (1.17 g, 18 mmol) and yielded a yellow liquid (0.80 g, 52%). Rf = 0.73 (2:1
c-hex/EtOAc) 1H NMR (300 MHz, CDCl
3): δ 3.77 (s, 3H), 3.74 (s, 3H),
11
diethyl-2-diazopentanedioate:
The diazo compound 9b was synthesised from diethyl 2-acetylpentanedioate (1.94 mL, 9.0 mmol) and sodium azide (1.17 g, 18 mmol) and yielded a yellow liquid (1.13 g, 59%). Rf = 0.69 (2:1
c-hex/EtOAc) 1H NMR (500 MHz, CDCl
3): δ 4.17 (dt, J = 3.1 Hz, 7 Hz,
4H), 2.57 (m, 4H), 1.26 (td, J = 7.5 Hz, 3.5 Hz, 6H) ppm. 13C NMR (500
MHz, CDCl3): δ 172.55, 166.80, 60.92, 60.85, 32.64, 19.70, 14.62, 14.30, 13.82 ppm. This is
consistent with the reference.17
2.4 TBA[Fe] Catalysed IMCR:
2.4.1 TBA[Fe] Catalysed 6-Amino-4-pyrimidone Method:
Benzamidine (60.1 mg, 0.5 mmol, 1.0 eq.), isocyanide 2c (137.4 mg, 0.6 mmol, 1.2 eq.) and TBA[Fe] (10.3 mg, 0.025 mmol, 0.05 eq.) were dissolved in C2H4Cl2 (2 mL, 0.25 M) in a
dried and flushed Schlenk (Figure 4). Ethyl-2-diazoacetate (71.2 μL, 0.6 mmol, 1.2 eq.) was added and the reaction mixture was stirred at 80°C overnight. The mixture was diluted with EtOAc (20 mL) and transferred to a separatory funnel, where the organic layer was washed with saturated aqueous NH4Cl (20.0 mL) and brine (2x 20.0 mL). The organic layer was then
dried with Na2SO4, filtered and concentrated in vacuo. The catalyst was filtered using a flash
column (5% MeOH in CH2Cl2) and a crude yield was determined using dimethylfurone (26.6
μL) as IS. The crude was purified with flash chromatography (3% MeOH in CH2Cl2). This
method was also performed with 3c as starting material (Figure 4).
6-((2-iodophenyl)amino)-2-phenylpyrimidin-4(3H)-one:
The 6-amino-4-pyrimidone 2’ was synthesised from isocyanide 2c (137.4 mg, 0.6 mmol, 1.2 eq.), benzamidine (60.1 mg, 0.5 mmol, 1.0 eq.) and ethyl-2-diazoacetate (71.2 μL, 0.6 mmol, 1.2 eq.) and yielded a dark-brown solid. 1H NMR (500 MHz, CDCl
3): δ 6.97 (s,
1H) ppm as characteristic peak and the IS dimethylfurone indicated a yield of 8%. m/z calculated for C16H12IN3O [M+H+]: 490.0, found
490.
2.4.2 TBA[Fe] Catalysed Methyl-2-isocyanobenzoate Method:
Methyl-2-isocyanobenzoate 4c (80.6 mg, 0.5 mmol, 1.0 eq.) and TBA[Fe] (10.3 mg, 0.025 mmol, 0.05 eq.) were dissolved in C2H4Cl2 (2 mL, 0.25 M) in a dried and flushed Schlenk
(Figure 4). Ethyl-2-diazoacetate (71.5 μL, 0.5 mmol, 1.0 eq.) and propylamine (49.3 μL, 0.6 mmol, 1.2 eq.) were added and the reaction mixture was stirred at 80°C with monitoring with TLC. After 30 minutes DBU (74.7 μL, 0.5 mmol, 1.0 eq.) was added and changes were monitored with TLC, after another 30 minutes TBOK (22.4 mg, 0.2 mmol, 0.4 eq.) was added. The reaction mixture was diluted with EtOAc (40 mL) after 30 minutes and transferred to a separatory funnel, where it was washed with saturated aqueous NH4Cl4 (40.0 mL), water (40.0
mL) and brine (40.0 mL). The organic layer was then dried with MgSO4, filtered and
concentrated in vacuo.
3. Discussion
3.1 Isocyanide Synthesis:
Isocyanides 2c-4c (Figure 4) were synthesised using the formamide dehydration method (Scheme 6.1). Formamide 2b had a high yield for the formamide step with 89% and the NMR spectra showed that the correct product was formed with high purity. The dehydration step lowered the total yield of isocyanide 2c drastically to 3%. The TLC monitoring showed that the reaction had proceeded, leaving the purification by recrystallisation as the probable cause. After concentration in vacuo of the crude a dark green oil remained, in contrast to the
12 light green crystals that were isolated after recrystallization, which severely complicated the recrystallization process. Two recrystallizations were attempted with minor success, yielding the product in a low 3%. The paper wherein this procedure was previously employed also reported a solid crude and a colourless solid after purification, indicating that impurities were present in the crude to prevent crystallization.12 The green colouration was present before the
workup which means that something during the dehydration went wrong which produced enough of the impurity. Besides impurities the solvents used during the reaction and workup, DCM and water, most likely aren’t the cause of the oily crude since all DCM would’ve been boiled off under vacuum and there wouldn’t have been enough water after washing with brine and vacuum drying.
Both formamides 3b and 4b were synthesised in similar high yields to formamide 2b and their NMR spectra showed that the desired product was formed with high purity. Isocyanide 3c was synthesised with a decent total yield (43%), however, even after purification the NMR spectrum shows some type of impurity (Figure 4). Unlike the formamide 3b rotamers shouldn’t be present in the spectrum of 3c due to the absence of the formamide group, however there are extra peaks present at a significant intensity at a ratio compared to the main product of 0.6:1. These peaks do not correspond to literature values of the 9-aminofluorene or formamide 3b, nor do they correspond to the other reagents or solvents used, leaving a potential side-reaction as the remaining candidate. Lastly isocyanide 4c was synthesised with high yield and purity according to the NMRs with nothing further of note.
Isocyanides 2c and 4c were also synthesised using the difluorocarbene method (Scheme 6.2), along with isocyanides 5c and 6c (Figure 4). According to TLC monitoring and NMRs however 2c, 4c and 5c failed to yield any products. According to Zhang et al. electron poor aniline derivatives fail to produce isocyanides in significant quantities.8 This happens
because, according to the mechanism proposed in their paper (Scheme 7), the difluorocarbene undergoes a nucleophilic attack by the amine, which requires the aniline to be sufficiently electron-rich. The anilines 2a, 4a and 5a all contain electron withdrawing groups: an ortho halo group, ortho methoxycarbonyl group and para trifluoromethyl group respectively, which would explain the lack of isocyanide products.
Isocyanide 6c was formed with a decent yield but proton NMR showed impurities even after purification by silica column (Figure 4). A primary amine attached to a furan molecule was shown to work in the paper and thus the thiophene version was expected to work as well.
When comparing the formamide dehydration method with the difluorocarbene method it seems that the scope of the former is more extensive than the latter, successfully synthesising isocyanides from amines that didn’t work with the latter method. Despite this the difluorocarbene method has the advantage of being a single step synthesis, which drastically decreases workload. The lack of dangerous dehydrating agents like phosphorus oxychloride in the difluorocarbene method gives yet another advantage, which makes this method a viable alternative to the formamide dehydration method. Ideally the difluorocarbene method would be used if the primary amine is an alkyl or an electron-rich aryl while the traditional formamide dehydration method is used on electron-poor aryl amines.
13 The ribose isocyanide 7c required a slightly different path, with the direct method consisting of a Leuckart-Wallarch reductive amination approach recently published by Dömling et al. that’s been applied to pyranoses followed by the traditional dehydration step (Scheme 10).18 This approach yielded a brown syrup, according to proton NMRs the crude was a
complex mixture of products but the MS showed that the formamide was present in some capacity (m/z calculated for C27H29NO2 [M+H+] 448.20, found 448). The original paper
employing this method by Dömling et al. only used it to prepare pyranose formamides, which resulted in colourless solids, and not to prepare furanose formamides. Flash chromatography was eventually performed but 7b could not be isolated. A more traditional pathway was planned out, with the unprotected alcohol 7a being tosylated (7.1) and substituted with an azide transfer (7.2), after which it would be reduced to an amine (7.3) and would then undergo the traditional formamide dehydration approach (Scheme 10). A general tosylation method failed to yield any tosylated alcohol according to proton NMR.19 A second tosylation method
specifically for sugars was then employed which also failed to produce any tosylated alcohols, this method was performed again with higher molar concentrations (1.0 M) with similar results.20
3.2 Alpha-diazo Ester Synthesis:
The diazo esters 8b and 9b (Figure 4) were synthesised with the Danheiser variation of the sulfonyl-azide-free approach by Krasavin et al. (Scheme 9) which yielded both compounds in high yields as yellow oils, with both proton NMRs indicating high purity. More generally, according to the original paper the standard SAFE method shows an impressive scope and consistency in yields.10
3.3 Carbene Transfer Reactions:
The isocyanides 2c and 3c (Figure 4) were employed in the standard TBA[Fe] catalysed carbene transfer reaction described in the experimental. 6-Amino-4-pyrimidone 2’ (Scheme 11.1) was present in the crude in low yield according to proton NMR and its mass was also present on the HRMS. Proton NMR showed that isocyanide 3c did not convert into the ketenimine due to a missing characteristic peak. Isocyanide 4c (Scheme 11.3) was employed in the same reaction but with the amidine swapped for a primary propyl amine along with two increasingly strong bases. According to the proton NMR this reaction did not yield any of the desired product 4” (Scheme 11.3) as it lacked a characteristic peak. Furthermore, the HRMS indicates that the major product comes from isocyanide 4c undergoing a transesterification with the propyl amine (m/z found 189, m/z calculated for C11H12N2O [M+H+]
14 189.09). These initial test reactions show that only isocyanide 2c reacts to a certain extent in the carbene transfer reaction.
3.4 Potential Future Applications
For potential future applications, the 6-amino-4-pyrimidone 2’ could be turned into the fused ring scaffold 2” through a substitution reaction with the iodine (Scheme 11.1). The alpha-diazo diesters 8b and 9b (Figure 4) could be employed in the carbene transfer reaction to yield 6-amino-4-pyrimidones 8’ and 9’ which could react in the presence of a lewis acid to form the scaffolds 8” and 9” (Scheme 11.2). If the methyl-2-isocyanobenzoate could form the ketenimine intermediate 4d its three electrophilic centers could result in a divergent synthesis method, with the addition of benzamidine yielding the expected 6-amino-4-pyrimidone 4’. But a primary amine like propyl amine would likely favour reacting with the other electrophilic center form new scaffold 4” (Scheme 11.3), as reacting with the other electrophilic center would result in a 4-membered ring. Lastly if the isocyanide 7c (Figure 4) reacts in the carbene transfer reaction its resulting 6-amino-4-pyrimidone 7’ could serve as a precursor to the adenosine derivative 7”, which has shown promise as a chemical probe for the methyl transferase enzyme PRMT5 (Scheme 11.4).21
4. Conclusion
Several isocyanides and diazo compounds were synthesised, using varying methods, to later be employed in the further exploration of the TBA[Fe] catalysed 6-amino-4-pyrimidone MCR, with a focus on interesting potential products and post-reaction modifications. Both the traditional Ugi formamide and novel Zhang difluorocarbene methods were used, which mostly produced the desired isocyanides in decent yields but indicated that the Ugi approach has a more reliable, more expansive scope. Nevertheless the difluorocarbene approach’s less resource intensive, time-saving, saver method should be used when the desired isocyanide is included or expected to be within its scope. A ribose based isocyanide was also planned but both the traditional and Leuckart-Wallach approaches experienced difficulties, with the latter seeming more promising if the problem of isolating the desired formamide can be overcome.
Scheme 11: Top to bottom, Ring-closing through post-MCR Substitution & through post-MCR esterification, n = 1,2. Standard and alternative ring-closing ketenimine with primary amine, Synthesis of Adenosine derivative
15 The Danheiser variant of the SAFE protocol was also used to produce two diazo compounds with good yields and purities, with the original paper indicating a reliable, wide scope for diazo esters specifically. Several of the isocyanides were employed in the IMCR with only one yielding the desired product.
5. Acknowledgements
I would like to thank dr. Eelco Ruijter for allowing me to perform it at their research group. I’d mainly like to thank my daily supervisors Daniël Preschel and Tom Roose for helping me when needed as well as answering my questions. I’d also like to thank Helena Tejedor for helping out at the lab and getting me situated during my daily supervisors’ absences in the first week. Lastly I’d like to thank the entire SyBOrCh group for being accommodating and being an overall nice place to work at.
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