The Mannich reaction in the synthesis of N,S-containing heterocycles : 55*5. Synthesis and structures of new pyrimido[2,1-b][1,3,5] thiadiazine derivatives

Article abstract of DOI:10.1007/s11172-007-0218-6

Reactions of 6-aryl-5-cyano-4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidines with formaldehyde and primary amines gave earlier unknown 3,4-dihydro-2H,6H- pyrimido[2,1-b]-[1,3,5]thiadiazine derivatives in 58-94% yields. In boiling AcOH, these pyrimidothiadiazines underwent the retro-Mannich reaction leading to the starting pyrimidine-2-thiones. The structure of 3-(4-ethoxyphenyl)-6-oxo-8- phenyl-3,4-dihydro-2H,6H-pyrimido[2,1-b][1,3,5]thiadiazine-7-carbonitrile was studied by X-ray diffraction analysis.

Full text of DOI:10.1007/s11172-007-0218-6

Russian Chemical Bulletin, International Edition, Vol. 56, No. 7, pp. 1437—1440, July, 2007
1437
The Mannich reaction in the synthesis of N,Sꢀcontaining heterocycles
5.* Synthesis and structures of new
pyrimido[2,1ꢀb][1,3,5]thiadiazine derivatives
V. V. Dotsenko,aꢀ S. G. Krivokolysko,a E. B. Rusanov,b and V. P. Litvinovc†
aChemEx Laboratory, V. Dal´ EastꢀUkrainian National University,
20a Molodyozhny kv., 91034 Lugansk, Ukraine.
Fax: + 380 (0642) 41 9151. Eꢀmail: ksg@lep.lg.ua
bInstitute of Organic Chemistry, National Academy of Sciences of Ukraine,
5 ul. Murmanskaya, 02094 Kiev, Ukraine.
Fax: + 380 (044) 573 2643. Eꢀmail: iochkiev@ukrpack.net
cN. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences,
47 Leninsky prosp., 119991 Moscow, Russian Federation.
Fax: +7 (495) 135 8837
Reactions of 6ꢀarylꢀ5ꢀcyanoꢀ4ꢀoxoꢀ2ꢀthioxoꢀ1,2,3,4ꢀtetrahydropyrimidines with formalꢀ
dehyde and primary amines gave earlier unknown 3,4ꢀdihydroꢀ2H,6Hꢀpyrimido[2,1ꢀb]ꢀ
[1,3,5]thiadiazine derivatives in 58—94% yields. In boiling AcOH, these pyrimidothiadiazines
underwent the retroꢀMannich reaction leading to the starting pyrimidineꢀ2ꢀthiones. The strucꢀ
ture of 3ꢀ(4ꢀethoxyphenyl)ꢀ6ꢀoxoꢀ8ꢀphenylꢀ3,4ꢀdihydroꢀ2H,6Hꢀpyrimido[2,1ꢀb][1,3,5]thiaꢀ
diazineꢀ7ꢀcarbonitrile was studied by Xꢀray diffraction analysis.
Key words: the Mannich reaction, 6ꢀarylꢀ5ꢀcyanoꢀ4ꢀoxoꢀ2ꢀthioxoꢀ1,2,3,4ꢀtetraꢀ
hydropyrimidines, formaldehyde, primary amines, pyrimido[2,1ꢀb][1,3,5]thiadiazines, the
retroꢀMannich reaction, Xꢀray diffraction analysis.
The chemistry of 1,3,5ꢀthiadiazine derivatives is a
promising and developing research area.1 In the last few
years, fused 1,3,5ꢀthiadiazines have become of considerꢀ
able interest because of, on the one hand, the accessibility
of the starting 2ꢀmercaptoazoles and ꢀazines and, on the
other hand, a wide palette of practical applications of
compounds of this group. In particular, symmꢀtriazoꢀ
lo[3,4ꢀb][1,3,5]thiadiazine derivatives2—5 and substituted
thiazolo[3´,4´:1,5][1,2,4]triazolo[3,4ꢀb][1,3,5]thiadiaziꢀ
nes6 have antibacterial and fungicidal effects, respectively,
and [1,3,5]thiadiazino[3,2ꢀa]benzimidazole derivatives
exhibit herbicidal and insecticidal activities.7 According
to patented data,8 some imidazoꢀ and pyrimido[2,1ꢀb]ꢀ
[1,3,5]thiadiazines are broadꢀspectrum pesticides. Thus,
the synthesis of novel compounds of this type is of current
interest.
has been used earlier to obtain thiadiazines fused with
1,2,4ꢀtriazole,2—6,9—12 imidazole, 1,2,4ꢀtriazine,13 and
benzimidazole rings.14 In this way, we have recently synꢀ
thesized for the first time pyrido[2,1ꢀb][1,3,5]thiadiazine15
and imidazo[2,1ꢀb][1,3,5]thiadiazine derivatives.16 Since
this approach is simple and highly efficient and involves
accessible starting reagents, it seems to be promising for
combinatorial chemistry. Proceeding further in these inꢀ
vestigations, we studied the behavior of accessible17 6ꢀarylꢀ
5ꢀcyanoꢀ4ꢀoxoꢀ2ꢀthioxoꢀ1,2,3,4ꢀtetrahydropyrimidines
1a,b under the conditions of the "double" Mannich conꢀ
densation.
We found that reactions of thioxopyrimidines 1 with
primary aromatic amines and an excess of formaldehyde
in EtOH give new pyrimido[2,1ꢀb][1,3,5]thiadiazines
2a—f in high yields (Scheme 1). The process is regioꢀ
selective: the cyclization involves the S—C(2)—N(3)H
fragment, while isomeric products (like structure 3) arising
from double aminomethylation at the S—C(2)—N(1)H
fragment were not detected. The order of addition of the
reagents did not affect the yield of the final product. For
instance, the yield of thiadiazine 2f was 60%, regardless of
whether we added formalin first to a suspension of
thioxopyrimidine 1b and then pꢀtoluidine or vice versa.
An assumed reaction mechanism involves the formation
Among the most popular and preparatively accessible
methods for construction of the 1,3,5ꢀthiadiazine system
is the multicomponent "double" Mannich cyclocondensaꢀ
tion of various 2ꢀmercaptoazoles and ꢀazines with priꢀ
mary amines and formaldehyde. For instance, this method
* For Part 4, see Izv. Akad. Nauk, Ser. Khim., 2007, 1014 [Russ.
Chem. Bull., Int. Ed., 2007, 56, 1053].
† Deceased.
Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1384—1387, July, 2007.
1066ꢀ5285/07/5607ꢀ1437 © 2007 Springer Science+Business Media, Inc.

1438
Russ.Chem.Bull., Int.Ed., Vol. 56, No. 7, July, 2007
Dotsenko et al.
Scheme 1
1: R = Ph (a), 4ꢀMeC6H4 (b);
2: R = Ph, Ar = 4ꢀEtOC6H4 (a); R = 4ꢀMeC6H4, Ar = 4ꢀEtOC6H4 (b); R = 4ꢀMeC6H4, Ar = 4ꢀFC6H4 (c); R = 4ꢀMeC6H4, Ar = 4ꢀClC6H4 (d);
R = 4ꢀMeC6H4, Ar = 4ꢀBrC6H4 (e); R = Ar = 4ꢀMeC6H4 (f)
at the first step of the corresponding Nꢀ(hydroxyꢀ
methyl)amines 4, which react with thiones 1a,b to give
intermediate 5a or 5b (the formation of these intermediꢀ
ates is consistent with the regioselectivity of the process).
The initial N(3)ꢀaminomethylation of pyrimidinethiones
1a,b is supported by numerous data18 on aminomethylaꢀ
tion of structurally similar cyclic thioamides (5ꢀsubstiꢀ
tuted thiohydantoins and rhodanines). At the same time,
under the conditions of the Mannich reaction, analoꢀ
gous substrates (2ꢀthiouracil18 and 6ꢀmethylꢀ3ꢀthioxoꢀ
3,4ꢀdihydroꢀ1,2,4ꢀtriazinꢀ5(2H )ꢀone13) undergo only
Sꢀaminoalkylation, which suggests possible heterocyclizaꢀ
tion through intermediate 5a. It should be noted that
6ꢀmethylꢀ2ꢀthiouracil, a structural analog of thioxoꢀ
pyrimidines 1, does not react under these conditions and
its crystals are recovered unchanged from the reaction
mixture.
However, the scope of this synthesis of pyrimiꢀ
do[2,1ꢀb][1,3,5]thiadiazines is restricted to sterically unꢀ
hindered reactive amines. For instance, we failed to use
in this reaction amines with bulky substituents (tertꢀbutylꢀ
amine, 2ꢀethylꢀ6ꢀmethylaniline, and 2,6ꢀxylidine). In an
attempt to obtain analytically pure pyrimidothiadiazines
2a and 2f by recrystallization from glacial AcOH, we
found that the acid causes partial decomposition of the
1,3,5ꢀthiadiazine ring. According to TLC data, the
retroꢀMannich reaction leading to pyrimidine derivatives
1a,b was completed in 10 min when refluxing a solution
of compound 2a or 2f in AcOH.
IR spectra of pyrimidothiadiazines 2a—f show no abꢀ
sorption bands due to the N—H stretching vibrations.
The absorption bands due to the stretching vibrations of
the cyano and carbonyl groups appear at 2223—2210 and
1657—1640 cm–1, respectively. The absorption bands due
to the C=N stretching vibrations in the pyrimidine ring
appear at 1615—1605 cm–1. Apart from the characteristic
signals for the aromatic substituents, the 1H NMR spectra
of compounds 2a—f exhibit two broadened peaks at
δ 5.40—5.47 and 5.65—5.74. These are unresolved (at
200 MHz) multiplets relating to the C(2)H2 and C(4)H2
protons.
To elucidate the regiodirectivity of the reaction and
unambiguously choose between alternative structures 2
and 3, we examined structure 2a by Xꢀray difꢀ
fraction analysis. The general view of the molecule
is shown in Fig. 1. The central bicyclic system
C(1)—C(7)N(1)—N(3)S(1) in structure 2a is nonplanar.
The pyrimidinone ring is slightly twisted: the maximum
deviation of the atoms from the rootꢀmeanꢀsquare plane
is 0.043(1) Å; the bond length distribution in this ring is
characteristic of conjugated systems. The heterocycle
N(1)N(3)C(5)C(6)S(1) is nonplanar because of its

Pyrimido[2,1ꢀb][1,3,5]thiadiazines
Russ.Chem.Bull., Int.Ed., Vol. 56, No. 7, July, 2007
1439
C(22)
N(4)
C(14)
C(2)
O(2)
C(21)
C(12)
C(13)
C(17)
O(1)
C(3)
N(1)
C(18)
C(19)
C(8)
C(11)
C(1)
C(10)
C(16)
C(15)
C(9)
N(2)
C(6)
C(20)
C(5)
N(3)
C(7)
S(1)
Fig. 1. General view of structure 2a.
pension of an appropriate pyrimidineꢀ2ꢀthione 1a,b (2 mmol) in
EtOH (15 mL). The mixture was heated with stirring to comꢀ
plete dissolution and then an appropriate primary amine
(2.2 mmol) was added in one portion. The resulting mixture was
refluxed with vigorous stirring for 3 min and then stirred at
~20 °C for 4 h. The precipitate of pyrimidothiadiazine 2a—f was
filtered off and washed three times with EtOH.
unsaturation and exists in the envelope conformation: the
C(5)—C(7)N(1)S(1) atoms form a plane (the rootꢀmeanꢀ
square deviations of the atoms from this plane do not
exceed 0.036(1) Å) with which the plane formed by the
C(6), C(7), and N(3) atoms makes an angle of 57.9°. It is
characteristic that the conjugation of the lone electron
pairs of the S atom with the conjugated system of the
pyrimidine ring results in a large difference between the
S(1)—C(5) and S(1)—C(7) bond lengths (1.744(4) and
1.839(4) Å, respectively). The N(3) atom has a pyramidal
configuration; the sum of the bond angles at this atom is
345.5(3)° and the bond lengths are 1.431—1.434(3) Å.
In conclusion, the threeꢀcomponent Mannich reacꢀ
tion of 6ꢀarylꢀ5ꢀcyanoꢀ4ꢀoxoꢀ2ꢀthioxoꢀ1,2,3,4ꢀtetraꢀ
hydropyrimidines with formaldehyde and primary amines
is an efficient and simple regioselective route to novel
3,4ꢀdihydroꢀ2H,6Hꢀpyrimido[2,1ꢀb][1,3,5]thiadiazine
derivatives.
3ꢀ(4ꢀEthoxyphenyl)ꢀ6ꢀoxoꢀ8ꢀphenylꢀ3,4ꢀdihydroꢀ2H,6Hꢀ
pyrimido[2,1ꢀb][1,3,5]thiadiazineꢀ7ꢀcarbonitrile (2a). Yield 94%,
yellow crystals, m.p. 197—199 °C (Me2CO—PriOH (2 : 1)).
Found (%): C, 64.50; H, 4.62; N, 14.40. C21H18N4O2S. Calcuꢀ
lated (%): C, 64.60; H, 4.65; N, 14.35. IR, ν/cm–1: 2210 (CN);
1640 (C=O); 1615 (C=N). 1H NMR, δ: 1.33 (t, 3 H, CH3CH2O,
3J = 7.0 Hz); 3.94 (q, 2 H, CH3CH2O, 3J = 7.0 Hz); 5.40, 5.66
(both m, 2 H each, C(2)H2 and C(4)H2); 6.90 (q, 4 H,
3
4ꢀEtOC6H4, J = 9.0 Hz); 7.49 (m, 3 H, Ph, C(3)H—C(5)H);
7.90 (br.d, 2 H, Ph, C(2)H and C(6)H, 3J = 7.6 Hz).
3ꢀ(4ꢀEthoxyphenyl)ꢀ8ꢀ(4ꢀmethylphenyl)ꢀ6ꢀoxoꢀ3,4ꢀdihydroꢀ
2H,6Hꢀpyrimido[2,1ꢀb][1,3,5]thiadiazineꢀ7ꢀcarbonitrile (2b).
Yield 63%, light yellow needles, m.p. 207—209 °C. Found (%):
C, 64.99; H, 4.93; N, 13.95. C22H20N4O2S. Calculated (%):
C, 65.33; H, 4.98; N, 13.85. IR, ν/cm–1: 2218 (CN); 1646
(C=O); 1610 (C=N). 1H NMR, δ: 1.33 (t, 3 H, CH3CH2O, 3J =
7.1 Hz); 2.41 (s, 3 H, Me); 3.93 (q, 2 H, CH3CH2O, 3J =
7.1 Hz); 5.40, 5.65 (both m, 2 H each, C(2)H2 and C(4)H2);
6.93 (q, 4 H, 4ꢀEtOC6H4, 3J = 9.1 Hz); 7.28 (d, 2 H, 4ꢀMeC6H4,
Experimental
1
H NMR spectra were recorded on a Varian Gemini 200
instrument (200 MHz) in DMSOꢀd6 with Me4Si as the internal
standard. IR spectra were recorded on an IKSꢀ29 spectrophoꢀ
tometer (in Nujol). Elemental analysis was carried out on a
Perkin—Elmer C,H,NꢀAnalyser instrument. The purity of the
compounds obtained was checked by TLC on Silufol UV 254
plates in acetone—heptane (1 : 1). Spots were visualized in the
iodine vapor or under UV light. Melting points were determined
on a Kofler hot stage and are given uncorrected. The starting
6ꢀarylꢀ5ꢀcyanoꢀ4ꢀoxoꢀ2ꢀthioxoꢀ1,2,3,4ꢀtetrahydropyrimidines
1a,b were prepared according to a known procedure17 and reꢀ
crystallized from AcOH.
3
H(3) and H(5), J = 8.3 Hz); 7.83 (d, 2 H, 4ꢀMeC6H4, H(2)
3
and H(6), J = 8.3 Hz).
3ꢀ(4ꢀFluorophenyl)ꢀ8ꢀ(4ꢀmethylphenyl)ꢀ6ꢀoxoꢀ3,4ꢀdihydroꢀ
2H,6Hꢀpyrimido[2,1ꢀb][1,3,5]thiadiazineꢀ7ꢀcarbonitrile (2c).
Yield 58%, colorless crystals, m.p. 235—237 °C (Me2CO).
Found (%): C, 63.59; H, 3.99; N, 14.85. C20H15FN4OS. Calcuꢀ
lated (%): C, 63.48; H, 4.00; N, 14.81. IR, ν/cm–1: 2223 (CN);
1657 (C=O); 1608 (C=N). 1H NMR, δ: 2.42 (s, 3 H, Me); 5.43,
5.70 (both m, 2 H each, C(2)H2 and C(4)H2); 7.00—7.19 (m,
3
4 H, 4ꢀFC6H4); 7.27 (d, 2 H, 4ꢀMeC6H4, H(3) and H(5), J =
3,8ꢀDiarylꢀ6ꢀoxoꢀ3,4ꢀdihydroꢀ2H,6Hꢀpyrimido[2,1ꢀb]ꢀ
[1,3,5]thiadiazineꢀ7ꢀcarbonitriles 2a—f (general procedure). An
excess of aqueous 37% HCHO (5—6 mL) was added to a susꢀ
8.3 Hz); 7.84 (d, 2 H, 4ꢀMeC6H4, H(2) and H(6), 3J = 8.3 Hz).
3ꢀ(4ꢀChlorophenyl)ꢀ8ꢀ(4ꢀmethylphenyl)ꢀ6ꢀoxoꢀ3,4ꢀdihydroꢀ
2H,6Hꢀpyrimido[2,1ꢀb][1,3,5]thiadiazineꢀ7ꢀcarbonitrile (2d).

1440
Russ.Chem.Bull., Int.Ed., Vol. 56, No. 7, July, 2007
Dotsenko et al.
Yield 59%, colorless crystals, m.p. 251—253 °C. Found (%):
C, 60.93; H, 3.80; N, 14.29. C20H15ClN4OS. Calculated (%):
C, 60.83; H, 3.83; N, 14.19. IR, ν/cm–1: 2222 (CN); 1655
(C=O); 1605 (C=N). 1H NMR, δ: 2.42 (s, 3 H, Me); 5.45, 5.73
(both m, 2 H each, C(2)H2 and C(4)H2); 7.20 (q, 4 H, 4ꢀClC6H4,
tions with I > 2σ(I ). The residual electron densities in the final
refinement cycle were 0.50 and –0.25 e Å–3. Comprehensive
Xꢀray diffraction data for compound 2a have been deposꢀ
ited with the Cambridge Crystallographic Data Center
(CCDC 610045; CCDC, 12 Union Road, Cambridge CB2 1EZ,
UK, fax: +44ꢀ1223/336ꢀ033; eꢀmail: deposit@ccdc.cam.ac.uk,
http://www.ccdc.cam.ac.uk).
3
3J = 8.0 Hz); 7.29 (d, 2 H, 4ꢀMeC6H4, H(3) and H(5), J =
8.2 Hz); 7.84 (d, 2 H, 4ꢀMeC6H4, H(2) and H(6), 3J = 8.2 Hz).
3ꢀ(4ꢀBromophenyl)ꢀ8ꢀ(4ꢀmethylphenyl)ꢀ6ꢀoxoꢀ3,4ꢀdihydroꢀ
2H,6Hꢀpyrimido[2,1ꢀb][1,3,5]thiadiazineꢀ7ꢀcarbonitrile (2e).
Yield 59%, colorless crystals, m.p. 262—264 °C. Found (%):
C, 54.50; H, 3.42; N, 12.85. C20H15BrN4OS. Calculated (%):
C, 54.68; H, 3.44; N, 12.75. IR, ν/cm–1: 2219 (CN); 1645
(C=O); 1610 (C=N). 1H NMR, δ: 2.42 (s, 3 H, Me); 5.47, 5.74
(both m, 2 H each, C(2)H2 and C(4)H2); 7.12, 7.43 (both d,
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3
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and H(6), 3J = 8.1 Hz).
Synthesis of 6ꢀarylꢀ5ꢀcyanoꢀ4ꢀoxoꢀ2ꢀthioxoꢀ1,2,3,4ꢀtetraꢀ
hydropyrimidines 1a,b from pyrimido[2,1ꢀb][1,3,5]thiadiazines
2a,f. A solution of pyrimidothiadiazine 2a or 2f (1.5 mmol) in
AcOH (10—15 mL) was refluxed for 10 min and then kept at
~20 °C for 5 days. The precipitate was filtered off and washed
with EtOH. The yield of tetrahydropyrimidine 1a was 56%, m.p.
305—310 °C (decomp.) (cf. Ref. 17: m.p. 300—302 °C). The
yield of tetrahydropyrimidine 1b was 53%, m.p. 295—300 °C
(decomp.) (see Ref. 17: m.p. 290—291 °C). Both products were
identical with samples described earlier.
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Enraf—Nonius CADꢀ4 automatic fourꢀcircle diffractometer
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θ
= 64.9°, sphere segment –1 < h < 10, –1 < k < 33,
max
–1 < l < 16). The total number of reflections was 3969. Crystals
of compound 2a are orthorhombic: a = 9.349(2) Å, b =
28.684(7) Å, c = 14.212(4) Å, V = 3811.3(16) Å3, Z = 8, dcalc
=
1.361 g cm–3, µ = 1.715 cm–1, F(000) 1632, space group Pnca.
The structure was solved by the direct method and refined by the
leastꢀsquares method in the fullꢀmatrix anisotropic approximaꢀ
tion with the SHELXS97 and SHELXL97 programs.19,20 In reꢀ
finement, 3130 reflections were used (2079 reflections with
I > 2σ(I )); the number of parameters refined was 254; the
number of reflections per parameter was 8.18; the weighting
2
2
scheme was ω = 1/[σ (F0 ) + (0.1127P)2 + 1.4562P], where
2
2
P = (F0 + 2Fc )/3; max. (mean) shift/esd in the final cycle
was 0.0011 (0.001). Calculations were corrected for anomalous
scattering; PSI scan semiempirical absorption correction was
applied (Tmin = 0.4677, Tmax = 0.7001). All hydrogen atoms
were objectively located from the electron density difference map
and refined isotropically. Final residuals were R1(F 2) = 0.0964
and Rw(F 2) = 0.2018, GOF = 1.055 for all reflections and
R1(F ) = 0.0601 and Rw(F 2) = 0.1739, GOF = 1.055 for reflecꢀ
Received July 3, 2006;
in revised form April 25, 2007