Dearomatization of 3,5-dinitropyridines - an atom-efficient approach to fused 3-nitropyrrolidines

Article abstract of DOI:10.24820/ark.5550190.p010.185

An efficient and convenient one-step method for the synthesis of decahydrodipyrrolo[3,4-b:3',4'-d]pyridine derivatives was developed on the basis of 1,3-dipolar cycloaddition of unstabilized N-methyl azomethine ylide with 2-substituted 3,5-dinitropyridine

Full text of DOI:10.24820/ark.5550190.p010.185

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Organic Chemistry
Arkivoc 2017, part iii, 181-190
Dearomatization of 3,5-dinitropyridines – an atom-efficient approach
to fused 3-nitropyrrolidines
Maxim A. Bastrakov,*a Anna Yu. Kucherova,a Alexey K. Fedorenko,a Alexey M. Starosotnikov,a
Ivan V. Fedyanin,b Igor L. Dalinger,a and Svyatoslav A. Shevelev a
a N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47,
Moscow 119 991, Russian Federation
b A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova st. 28,
Moscow, 119 991, Russian Federation
Email: b_max82@mail.ru
Dedicated to Professor Oleg A. Rakitin on the occasion of his 65th anniversary
Received 05-22-2017
Accepted 06-16-2017
Published on line 06-27-2017
Abstract
An efficient and convenient one-step method for the synthesis of decahydrodipyrrolo[3,4-b:3',4'-d]pyridine
derivatives was developed on the basis of 1,3-dipolar cycloaddition of unstabilized N-methyl azomethine ylide
with 2-substituted 3,5-dinitropyridines. This novel heterocyclic system contains two 3-nitropyrrolidine
fragments fused to a partially saturated pyridine ring. Such types of compound, as follows from the literature,
can be considered as potential nitric oxide donors.
Keywords: Dearomatization, 1,3-dipolar cycloaddition, azomethine ylides, fused pyrrolidines, NO donors, nitrogen-
oxygen systems, bridgehead nitro groups
DOI: https://doi.org/10.24820/ark.5550190.p010.185
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Introduction
The dearomatization of aromatic compounds is a valuable tool providing a variety of approaches to complex
hybrid biologically active molecules and analogues of naturally occurring compounds.1-3 In the last few
decades, a significant interest in dearomatization of heterocyclic compounds has been observed.2-4 This in turn
has influenced the development of synthetic organic chemistry: many reactions have been used for carbon-
carbon and carbon-heteroatom bond formation in the construction of prospective biologically active
compounds.4-6 Conversion of commercially available aromatics into functionalized alicyclic derivatives is
widely used as a strategy for the creation of valuable synthetic products. Among dearomatization methods,
1,3-dipolar cycloaddition is of particular interest. Recently, aromatic substrates (including heterocycles) have
been reported to undergo [3+2]-cycloaddition by C=C bonds as dipolarophiles with azomethine ylides
providing annulation of the pyrrolidine, pyrroline or pyrrole rings.7-10
The present work extends our ongoing research11-16 on the application of the dearomatization
methodology to the synthesis of novel nitrogen-oxygen systems17,18 – potential NO donors containing two or
more pharmacophoric fragments. Since the 1980s, when the unique role of NO in the regulation of numerous
physiological and pathophysiological processes was discovered, this small molecule has been of exceptional
interest.19,20 Search for new types of NO-donors is one of the actively developing areas of medical chemistry;
many papers have been published on the investigation of NO-releasing activity of different classes of
compound.21,22 For example, recent research shows 3-nitropyrrolidine fused with benzoazoles to be potential
NO-donors.23 This class of compound is quite limited and therefore insufficiently studied. In addition, the
pyrrolidine moiety (including fused pyrrolidines) is considered as a "privileged" structural fragment and a key
component of efficient organocatalysts,24 enzyme inhibitors,25 etc.
Our group has extensive experience in the synthesis of condensed 3-nitropyrrolidines via dearomative 1,3-
dipolar cycloaddition. Earlier26-29 we reported on the first example of [3+2]-cycloaddition of N-methyl
azomethine ylide 1 to the benzene ring of a number of m-dinitro-benzohetarenes 2. This resulted in
annulation of two pyrrolidine rings to the benzene ring and the formation of polycycles 3 (Scheme 1).
Scheme 1. [3+2]-Cycloaddition of N-methyl azomethine ylide to m-dinitrohetarenes.
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In addition, it has been reported9 that 3,5-dinitropyridine reacts with 3 equivalents of N-benzyl
azomethine ylide to give the tetracyclic derivative 4 (Scheme 2).
Scheme 2. [3+2]-Cycloaddition of N-benzyl azomethine ylide to 3,5-dinitropyridine.
To the best of our knowledge, this reaction constitutes the only example of an uncomplexed pyridine that
behaves as a two-electron component in a pericyclic cycloaddition process with azomethine ylides. However,
it was found that similar reaction of 3-nitropyridine or its N-oxide with N-benzyl azomethine ylide mainly
resulted in the recovery of unconsumed starting material.9
Results and Discussion
Taking into account the above-mentioned results we studied [3+2]-cycloaddition of ylide 1 to 2-substituted
3,5-dinitropyridines. The starting 2-substituted 3,5-dinitropyridines were synthesized from commercially
available 2-chloro-3,5-dinitropyridine 5 (Scheme 3). The chlorine atom in this compound can easily be
substituted with a variety of nucleophiles.30,31
Product
6a
RH
PhSH
Reaction conditions
Et3N, MeOH, 20 оС, 1 h
Et3N, MeOH, 20 оС, 1 h
Yield, %
94
6b
cyclo-С6Н11SН
87
6c
Et3N, MeOH, 20 оС, 1 h
83
6d
6e
i-BuSH
Et3N, MeOH, 20 оС, 1 h
81
93
PhOH
Na2CO3, CH3CN, reflux, 2 h
Scheme 3. Synthesis of 2-substituted 3,5-dinitropyridines.
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Compounds 6a-e were studied in reactions with the unstabilized azomethine ylide 1, which was generated
in situ from N-methylglycine and paraformaldehyde (Scheme 1). In all cases the products of double
cycloaddition of the dipole to aromatic C=C-NO2 fragments were isolated. (Scheme 4)
Scheme 4. [3+2]-Cycloaddition of N-methyl azomethine ylide to 2-substituted 3,5-dinitropyridines
In contrast to 2-unsubstituted 3,5-dinitropyridine 2 (Scheme 2), the C=N-bond in compounds 6a-e is
unreactive towards azomethine ylide. This result represents the first synthesis of derivatives of novel
heterocyclic system - decahydrodipyrrolo[3,4-b:3',4'-d]pyridine. It should be noted that hydrogenated
pyrrolo[3,4-c]pyridine core is an important scaffold since compounds of this class possess antibacterial32, and
anticancer activity33,34 as well as cognition activating properties.35
The structures of compounds 7a-e were confirmed by NMR-spectroscopy and HRMS data, as well as X-ray
diffraction study (for compounds 7a,b,e). It was found that addition of two molecules of the dipole occurs
from the opposite sides of the pyridine ring. A similar situation was observed earlier in the case of m-dinitro-
benzohetarenes,26 Scheme 1. The formation of cycloaddition products 7a-e was found to be
diastereoselective. In case of compounds 7a,b,e, the crystal and molecular structure (Figures 1 and 2)
confirmed the expected cis-addition of the dipole.
In all three compounds studied by X-ray diffraction the annelated five-membered rings and corresponding
nitro groups are located on opposite sides of the central heterocyclic fragment. Due to certain steric
hindrance, the six-membered rings in 7a and 7b have an envelope conformation with atom C5 (Figs. 1 and 2)
shifted by 0.520(2) and 0.473(2) Å from the mean plane of the remaining atoms. Only in 7e is the
conformation of the central ring close to a half-chair conformation, characteristic of cyclohexene.
Interestingly, the conformation of the annelated rings adjacent to the nitrogen atom N1 is a perfect
envelope with atom C11 out of the plane, and the conformation of the second cycle is intermediate between
an envelope and a half-chair. As expected, the nitrogen atoms of the five-membered rings are significantly
pyramidalized. Bond lengths and angles in the three compounds are typical to values for related fragments of
known substances. The maximal difference is observed for bond N1-C1 that is by 0.013 Å longer in sulfur-
~
containing molecules. All interactions between molecules in crystal are of weak van der Waals type. It is worth
noting that compounds 7e and 7a differ in only one atom (oxygen and sulfur), but they have completely
different crystal packing. This fact can be explained by different orientation of the phenyl substituent relative
to the central ring: the corresponding torsions N1-C2-O1-C13 and N1-C2-S1-C13 are equal to -34.26(1) and
24.47(1)° and have different signs.
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Figure 1. General view of molecules 7a (left) and 7e (right) in the crystal. Anisotropic displacement parameters
are drawn with 50% probability.
Figure 2. General view of molecule 7b in the crystal. Anisotropic displacement parameters are drawn with 50%
probability.
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Conclusions
In conclusion, a method for the synthesis of novel polycyclic system - 1,2,3,3a,5a,6,7,8,8a,8b-decahydro-
dipyrrolo[3,4-b:3’,4'-d]pyridine was elaborated based on 1,3-dipolar cycloaddition of unstabilized N-methyl
azomethine ylide with 2-R-3,5-dinitropyridines. These compounds represent complex hybrid molecules which
can be considered as potential NO-donors having some other types of biological activity due to the presence
of pyrrolidine and tetrahydropyridine moieties.
Experimental Section
General. All chemicals were of commercial grade and used directly without purification. Melting points were
1
measured on a Stuart SMP 20 apparatus. H and 13C NMR spectra were recorded on a Bruker AM-300
spectrometer (at 300,13 and 75,13 MHz, respectively) in DMSO-d6 or CDCl3 with TMS as internal standard.
HRMS spectra were recorded on a Bruker micrOTOF II mass spectrometer using ESI. All reactions were
monitored by TLC analysis using ALUGRAM SIL G/UV254 plates, which were visualized by UV light.
X-ray. Data collection for all samples was performed on a Bruker APEX DUO diffractometer equipped with CCD
detector (graphite-monochromated MoKα radiation, λ = 0.71073 Å or CuKα radiation, λ =1.54178 Å). Frames
were integrated using the Bruker SAINT software package36 by a narrow-frame algorithm. A semiempirical
absorption correction was applied with the SADABS37 program using the intensity data of the equivalent
reflections. The structures were solved with direct methods and refined by the full-matrix least-squares
technique against F2hkl in anisotropic approximation with SHELX38 software package. Hydrogen atoms were
placed in calculated positions and refined in riding model with Uiso(Hm) = 1.2Ueq(Cm) for methyl groups and
Uiso(H) = 1.2Ueq(C) for all other hydrogen atoms. Detailed crystallographic information is provided in
Supplementary material. Structures were deposited to Cambridge Structural Database, CCDC 1550123-
1550125 contain the supplementary crystallographic data for this paper. These data can be obtained free of
charge via http://www.ccdc.cam.ac.uk/data_request/cif , or by e-mailing data_request@ccdc.cam.ac.uk, or by
contacting The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax:
+44(0)1223-336033.
General procedure for the synthesis of compounds 6a-d. An appropriate thiol (1 mmol) and Et3N (0.14 mL, 1
mmol) were added to a solution of 2-chloro-3,5-dinitropyridine (0.2 g, 1 mmol) in methanol (30 mL). The
reaction mixture was stirred at room temperature for 0.5—2 h until the starting compound was completely
consumed (TLC). Then mixture was poured into water and acidified with HCl (pH 4)). The precipitate that
formed was filtered off, washed with water to a neutral reaction and dried in air.
o
o
1
3,5-Dinitro-2-(phenylthio)pyridine (6a). Yellow crystals. Yield 94%, mp 143-145 С (lit.30 123-125 С). Н NMR
13
(300 MHz, DMSO-d6): δ 9.34 (d, J = 1 Hz, 1Н), 9.12 (d, J = 1 Hz, 1Н), 7.62-7.56 (m, 5Н Ph). С NMR (75 MHz,
DMSO-d6): δ 162.7, 147.8, 140.9, 140.2, 135.6, 130.3, 129.7, 129.5, 127.8.
2-(Cyclohexylthio)-3,5-dinitropyridine (6b). Yellow crystals. Yield 87%, mp 130-132 С. Н NMR (300 MHz,
DMSO-d6): δ 9.53 (d, J = 2 Hz, 1Н), 9.07 (d, J = 2 Hz, 1Н), 4.09-4.03 (m, 1H), 2.07-1.30 (m, 10Н). С NMR (75
o
1
13
MHz, DMSO-d6): δ 162.6, 147.7, 140.5, 139.9, 129.3, 43.2, 32.0, 31.8, 25.4, 25.0. Anal. calcd for C11H13N3O4S: C,
46.64; H, 4.63; N, 14.83; S, 11.32; found C, 46.62; H, 4.61; N, 14.86; S, 11.3%.
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o
1
2-[(2-Furylmethyl)thio]-3,5-dinitropyridine (6c). Yellow solid. Yield 83%, mp 140-141 С. Н NMR (300 MHz,
13
DMSO-d6): δ 9.62 (s, 1Н), 9.12 (s, 1Н), 7.61 (s, 1H), 6.49 (s, 1H), 6.42 (s, 1H), 4.70 (s, 2H). С NMR (75 MHz,
DMSO-d6): δ 161.7, 149.3, 147.7, 142.9, 140.6, 140.5, 129.5, 110.9, 109.2, 27.5. Anal. calcd for C10H7N3O5S: C,
42.71; H, 2.51; N, 14.94; found C, 42.82; H, 2.37; N, 14.72%.
2-(Isobutylthio)-3,5-dinitropyridine (6d). Brown solid. Yield 81%, mp 60-61 oС. 1Н NMR (300 MHz, DMSO-d6): δ
9.55 (d, J = 2 Hz, 1Н), 9.10 (d, J = 2 Hz, 1Н), 3.26 (d, J = 7 Hz, 1H), 2.00 (m, 1Н), 1.05 (d, J = 7 Hz, 6H). 13С NMR
(75 MHz, DMSO-d6): δ 163.1, 147.6, 140.8, 140.0, 129.3, 39.0, 27.4, 21.8. Anal. calcd for C9H11N3O4S: C, 42.02;
H, 4.31; N, 16.33; found C, 42.23; H, 4.19; N, 16.14%.
3,5-Dinitro-2-phenoxypyridine (6e). Phenol (0.28 g, 3 mmol) and Na2CO3 (0.32 g, 3 mmol) were added to a
solution of 2-cloro-3,5-dinitropyridine (0.61 g, 3 mmol) in acetonitrile (50 mL). The reaction mixture was
refluxed for 2 h until the starting compound was completely consumed (TLC), poured into a fivefold excess of
water, and acidified with HCl to pH 2. The precipitate that formed was filtered off, washed with water to a
o
o
1
neutral reaction and dried to give colorless crystals. Yield 93%, m.p. 163-165 С (lit.31 159 С). Н NMR (300
13
MHz, DMSO-d6): δ 9.26 (s, 2Н), 7.55-7.48 (m, 2H, Ph), 7.39-7.28 (m, 3Н, Ph). С NMR (75 MHz, DMSO-d6): δ
157.7, 152.0, 147.8, 139.6, 131.8, 130.1, 126.4, 121.7.
General procedure for the synthesis of compounds 7a-e. A mixture of an appropriate 2-substituted 3,5-
dinitropyridine (1 mmol), paraformaldehyde (0.18 g, 6 mmol), and sarcosine (0.54 g, 6 mmol) was refluxed in
toluene (30 mL), while adding paraformaldehyde (0.03 g, 1 mmol) and sarcosine (0.089 g, 1 mmol) every hour
until the starting compound was completely consumed (TLC), the mixture was cooled to room temperature.
The solvent was evaporated under reduced pressure, and the residue was purified by column chromatography
on MN Kieselgel 60 (0.04–0.063 mm/230–400 mesh) using CHCl3 as an eluent.
2,7-Dimethyl-5a,8b-dinitro-5-(phenylthio)-1,2,3,3a,5a,6,7,8,8a,8b-decahydrodipyrrolo[3,4-b:3’,4’-d]pyridine
(7a). Yellow crystals. Yield 68%, mp 92-94 oС. 1Н NMR (300 MHz, CDCl3): δ 7.55-7.40 (m, 5Н, Ph), 4.89-4.86 (m,
1Н), 4.23 (d, J = 11 Hz, 1Н), 3.62-3.48 (m, 3Н), 3.04-2.91 (m, 2Н), 2.65-2.61(m, 1Н), 2.32 (s, 3Н, CH3), 2.30 (s,
3Н, CH3), 2.15-2.12(m, 1Н). 13С NMR (75 MHz, CDCl3): δ 135.2, 129.5, 129.0, 127.0, 93.1, 92.1, 65.7, 62.3, 61.5,
61.0, 58.6, 45.3, 41.3, 40.7. HRMS (ESI): m/z calcd for C17H21N5O4S+H+: 392.1387; found: 392.1392.
5-(Cyclohexylthio)-2,7-dimethyl-5a,8b-dinitro-1,2,3,3a,5a,6,7,8,8a,8b-decahydrodipyrrolo[3,4-b:3’,4’-d]-
pyridine (7b). Brown crystals. Yield 56%, mp 110-112 oС. 1Н NMR (300 MHz, CDCl3): δ 4.94-4.96 (m, 1Н), 4.15 (
d, J = 12 Hz, 1Н), 3.85-3.49 (m, 4Н), 2.95 (t, J = 8 Hz, 1Н), 2.45-2.40 (m, 5Н), 2.31 (s, 3Н), 2.17-1.38 (m, 10Н). 13C
NMR (75 MHz, CDCl3): δ 93.8, 92.6, 66.3, 62.4, 60.9, 59.0, 45.2, 43.4, 41.7, 40.9, 32.6, 32.4, 26.0, 25.8, 25.7.
HRMS (ESI): m/z calcd for C17H27N5O4S+H+: 398.1857; found: 398.1854.
5-[(2-Furylmethyl)thio]-2,7-dimethyl-5a,8b-dinitro-1,2,3,3a,5a,6,7,8,8a,8b-decahydrodipyrrolo[3,4-b:3’,4’-
d]pyridine (7c). Brown solid. Yield 50%, mp 135-136 oС. 1Н NMR (300 MHz, CDCl3): δ 7.35 (s, 1H), 6.32 (d, J = 3
Hz, 1Н), 6.22 (d,J = 3 Hz, 1Н), 4.98-5.01 (m, 1Н), 4.24 (s, 2H), 4.10 ( d, J = 12 Hz, 1Н), 3.77 (t, J = 10 Hz, 1Н),
3.52-3.64 (m, 2H), 3.07 (d, J = 11 Hz, 1Н), 2.95 (t, J = 8 Hz, 1Н), 2.60 (dd, J = 10 Hz, J = 3 Hz, 1Н), 2.46 (d, J = 12
Hz, 1Н), 2.35 (s, 3H), 2.29 (s, 3H), 2.14 (t, J = 10 Hz, 1Н). 13C NMR (75 MHz, CDCl3): δ 155.7, 149.7, 142.4, 110.7,
108.4, 93.5, 92.6, 66.2, 62.3, 62.1, 61.0, 58.9, 45.0, 41.3, 40.9, 26.8. HRMS (ESI): m/z calcd for C16H21N5O5S+H+:
396.1336; found: 396.1323.
5-(Isobutylthio)-2,7-dimethyl-5a,8b-dinitro-1,2,3,3a,5a,6,7,8,8a,8b-decahydrodipyrrolo[3,4-b:3’,4’-dpyridine
o
(7d). Beige needles. Yield 38%, mp 98-99 С. 1Н NMR (300 MHz, CDCl3): δ 4.95 (m, 1Н), 4.18 (d, J = 12 Hz, 1Н),
3.78 (d, J = 10 Hz, 1Н), 3.53-3.58 (m, 2H), 3.11 (d, J = 10 Hz, 1Н) 2.93-3.00 (m, 2H), 2.78-2.85 (m, 1H), 2.59 (dd,
J = 10 Hz, J = 3 Hz, 1H), 2.44 (d, J = 12 Hz, 1H), 2.36 (s, 3H), 2.31 (s, 3H), 2.13 (t, J = 10 Hz, 1H), 1.86 (m, 1H),
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0.99 (d, J = 6 Hz, 6H). 13C NMR (75 MHz, CDCl3): δ 156.9, 93.8, 92.8, 66.2, 62.4, 60.9, 59.0, 45.2, 41.5, 40.9,
38.1, 28.3, 22.0. HRMS (ESI): m/z calcd for C15H25N5O4S+H+: 372.1700; found: 372.1688.
2,7-Dimethyl-5a,8b-dinitro-5-phenoxy-1,2,3,3a,5a,6,7,8,8a,8b-decahydrodipyrrolo[3,4-b:3’,4’-d]pyridine
o
1
(7e). Brown crystals. Yield 45%, mp 112-114 С. Н NMR (300 MHz, CDCl3): δ 7.39 (t, J = 8 Hz, 2H), 7.23 (t, J =
7Hz, 1H), 7.10 (d, J = 8 Hz, 2H) 5.02 (dd, 1Н, J = 7, 4 Hz), 4.13 (d, J = 12 Hz, 1Н), 3.66-3.51 (m, 3Н), 3.05-2.88 (m,
13
3Н), 2.47 (с, 3Н,CH3), 2.32 (s, 3Н, CH3). С NMR (75 MHz, CDCl3) δ: 153.1, 152.0, 129.6, 125.8, 121.4, 92.5,
89.3, 64.9, 63.0, 62.4, 59.0, 58.7, 46.8, 41.3, 41.1, 30.9. HRMS (ESI): m/z calcd for C17H21N5O5+H+: 376.1615;
found: 376.1607.
Acknowledgements
This work was supported by the Russian Science Foundation (grant no. 14-50-00126).
Supplementary Material
1H, 13C NMR and HRMS spectra of compounds 6 and 7, X-ray diffraction data for compounds 7a,b,e.
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