Synthesis and Structure of New Substituted Pyrimidinone with Unsaturated Side Chain

Article abstract of DOI:10.1134/S1070428018050160

Melting of a mixture of 5-substituted 2,4-dimethyl-1,6-dihydropyrimidin-6-ones with cinnamic aldehyde, 1-methylindoline-2,3-dione and 6-methoxy-2-chloroquinoline-3-carbaldehyde in the presence of ZnCl₂ led to the formation of substituted pyrimidines with conjugated bonds in the position 2. The structure of synthesized compounds as 2-isomers was confirmed by 2D ¹H NMR NOESY data.

Full text of DOI:10.1134/S1070428018050160

ISSN 1070-4280, Russian Journal of Organic Chemistry, 2018, Vol. 54, No. 5, pp. 771–775. © Pleiades Publishing, Ltd., 2018.
Original Russian Text © A.A. Harutyunyan, G.T. Gukasyan, H.A. Panosyan, R.A. Tamazyan, A.G. Aivazyan, G.G. Danagulyan, 2018, published in Zhurnal
Organicheskoi Khimii, 2018, Vol. 54, No. 5, pp. 766–770.
Synthesis and Structure of New Substituted Pyrimidinone
with Unsaturated Side Chain
A. A. Harutyunyana,b,* G. T. Gukasyana, H. A. Panosyanb, R. A. Tamazyanb,
A. G. Aivazyanb, and G. G. Danagulyana,b
a Russian–Armenian (Slavic) University, Yerevan, 0051 Armenia
*e-mail: harutyunyan.arthur@yahoo.com
b The Scientifical and Technological Centre of Organic and Pharmaceutical Chemistry,
National Academy of Sciences of Armenian Republic, Azatutyan pr. 26, Yerevan, 0014 Armenia
Received July19, 2017
Abstract—Melting of a mixture of 5-substituted 2,4-dimethyl-1,6-dihydropyrimidin-6-ones with cinnamic
aldehyde, 1-methylindoline-2,3-dione and 6-methoxy-2-chloroquinoline-3-carbaldehyde in the presence of
ZnCl2 led to the formation of substituted pyrimidines with conjugated bonds in the position 2. The structure of
synthesized compounds as 2-isomers was confirmed by 2D 1Н NMR NOESY data.
DOI: 10.1134/S1070428018050160
The interest to the synthesis of pyrimidines with a
system of unsaturated double bonds in the side chain is
due both to the high biological activity of styryl
derivatives of pyrimidines [1, 2] and to the optical
absorption and emission properties of heteroconjugated
pyrimidines [3]. Here we report on a series of new
substituted pyrimidines containing in the position 2 of
the pyrimidine ring 1-methyl-2-oxo-3-indolylidenemethyl,
2-(3-quinolyl)ethylene, and 1-phenyl-1,3-butadiene
groups. The initial 2,4-dimethyl-1,6-dihydropyrimidin-
6-ones 1a–1f were prepared by the reaction of 2-subs-
tituted ethyl 3-oxobutanoates [4] with acetamide in
anhydrous methanol in the presence of sodium
methylate. Pyrimidines 1a, 1c, and 1e–1g were syn-
thesized in [5], 1b, in [6].
The structure of 5-butyl-2,4-dimethyl-1,6-dihydro-
pyrimidin-6-one 1c was proved by X-ray diffraction
(XRD) analysis (Figs. 1, 2).
The heterocyclic fragment N1C2N3C4C5C6 is
practically planar with a maximum deviation from the
mean square plane 0.0091(3) Å. The molecules of
compound 1c form in the crystal centrosymmetric
cyclic dimers (Fig. 2) owing to intermolecular
hydrogen bonds N1–H1···O7 [the length of the donor-
acceptor bond is 2.804(2) Å].
The reaction of 5-substituted 2,4-dimethyl-1,6-dihyd-
ropyrimidin-6-ones 1a–1g with 1-methyl-indoline-2,3-
dione 2, 6-methoxy-2-chloro-3-quinolinecarbaldehyde
3, and cinnamic aldehyde 4 in the presence of ZnCl2
C8
O7
N1
N1'
H1'
C6
O7
C2
N3
C5
C10
C11
C12
O7'
H1
N1
C4
C9
C13
Fig. 2. Fragment of crystal packing of 5-butyl-2,4-dimethyl-
1,6-dihydropyrimidin-6-one 1c showing the formation of
centrosymmetric dimer.
Fig. 1. General arrangement of the molecule of 5-butyl-2,4-
dimethyl-1,6-dihydropyrimidin-6-one 1c by XRD data.
771

HARUTYUNYAN et al.
772
Scheme 1.
O
O
O
N
N
O
R
N
HN
2
3
4
5a_5c
O
N
O
O
O
HN
N
Cl
R
O
HN
ZnCl2
N
N
OH
1a_1g
6
O
CHO
R
HN
N
7a_7c
1, R = (CH2)2Me (a), CH2CH=CH2 (b), (CH2)3Me (c), CH(CH2)4 (d), CH2CH2CHMe2 (e), (CH2)5Me (f), Bn (g);
5, R = (CH2)3Me (a), CH(CH2)4 (b), Bn (c); 7, R = CH2CH=CH2 (a), (CH2)3Me (b), CH2CH2CHMe2 (c).
afforded 3-substituted 1-methylindolin-2-ones 5a–5c,
substituted 2-(3-quinolyl)-pyrimidone 6, and 5-sub-
stituted buta-1,3-dienyl-1,6-dihydropyrimidin-6-ones
7a–7c (Scheme 1).
indication of the prevailing formation of one among
regioisomeros (2- or 4-styryl-substituted pyrimidine),
yet such preliminary indications were obtained for
geometric isomers. In trans-isomers of compounds 5a–
5c unfavorable steric interactions were revealed
between the atoms H4 of isatin benzene ring and НN1
of pyrimidine in case of coplanar location of the
pyrimidine and isatin rings, whereas in the cis-isomers
such interactions are less significant (Fig. 3).
The condensation of 6-methoxy-2-chloro-3-
quinolinecarbaldehyde with pyrimidinone 1a is
accompanied with a hydrolytic substitution of the
chlorine atom in the position 2 of the quinolone ring
with the formation of quinolinol derivative 6. The
consideration of computer molecular models of
compounds 5a–5c (program product Cambridge Soft
Corporation Chem. 3D 5.0) did not give unambiguous
The comparison of the reactivity of groups 2- and 4
-СН3 of 1,6-dihydropyrimidin-6-one in the reactions
with carbonyl compounds where the methyl group
O
O
O
H
HN
R
R
N
HN
N
N
N
O
E-5a_5c
Z-5a_5c
Fig. 3. Molecular models of compounds 5a–5c.
RUSSIAN JOURNAL OF ORGANIC CHEMISTRY Vol. 54 No. 5 2018

SYNTHESIS AND STRUCTURE OF NEW SUBSTITUTED PYRIMIDINONE
773
Table 1. Main crystallographic characteristics and
experimental data for 5-butyl-2,4-dimethyl-1,6-dihydro-6-
pyrimidinone 1c
plays the role of a nucleophilic site with a partial
negative sign shows the greater chemical activity of
the 2-СН3 group due to more efficient delocalization of
the negative sign. The discussed assumptions were
proved by the study of NMR spectra of compounds 5a,
5c, and 7b.
Parameter
Empirical formula
Molecular mass
Crystal system
Space group
a, b, c, Å
Value
C10H16N2O
180.25
As show the 2D NOESY NMR spectra of
compounds 5a, 5c, and 7b the reaction proceeds at the
2-methyl group of the pyrimidine ring. It is confirmed
by the NOE between the 6-methyl and the group
α-CH2 of substituents in the position 5 of the ring.
Moreover, the presence of intensive NOE between the
proton of the exocyclic double bond and H4 of the
aromatic ring of 1- methylisatin shows that compounds
5a and 5c have Z-configuration.
Triclinic
P-1
4.8866(10), 10.088(2), 11.577(2)
α, β, γ, deg
114.58(3), 96.59(3), 90.66(3)
V, Å3
514.4(2)
Z
2
Dcalc, g/cm3
μ(MoKα), mm–1
F(000)
1.164
EXPERIMENTAL
0.076
196
IR spectra were recorded on a spectrophotometer
1
Crystal size, mm
Temperature, K
Radiation, Å
Θmin, θmax, deg
Scan range
0.18×0.23×0.35
Nicolet Avatar 330 in mineral oil. Н NMR spectra
were registered on a spectrometer Varian Mercury-300
at operating frequency 300 МHz in a mixture DMSO-
d6–CCl4, 1 : 3, internal reference TMS. Elemental
analysis was carried out on an automatic analyzer ЕА
3000 Eurovector (Italy). X-ray diffraction analysis was
performed on a single crystal of compound 1c at room
temperature using automatic diffractometer Enraf-
Nonius CAD-4 (graphite monochromator, МоKα-
radiation, θ/2θ-scanning). The structure was solved by
the direct method, hydrogen atoms coordinates were
partially found from the difference Fourier syntheses.
The coordinates of hydrogen atoms of methyl groups
were geometrically calculated and refined in the rider
model with the following restrictions: length of the
bond C–H 0.96 Å, Uiso(H) = 1.5 Ueq(C). The structure
was refined by full-matrix least-squares method in
anisotropic approximation for nonhydrogen atoms and
in isotropic approximation for hydrogen atoms. All
structural computations were carried out using
SHELXTL software [6]. TLC was performed on а
Silufol UV-254 plates, eluent ethanol–chloroform,
1 : 10, development in iodine vapor.
293
0.71073
2.0, 30.0
–6≤h=6, –14=k=14, –16=l=16
Number of measured
reflections
Observed reflections with
I > 3.0σ(I)
5966
1344
Nref, Npar
R, wR2, S
2983, 160
0.0593, 0.1609, 0.96
ethanol was added 0.95 g (0.01 mol) of preliminary
dried acetamidine hydrochloride and 0.01 mol of 2-
substituted ethyl 3-oxobutanoate. The mixture was
boiled for 6 h, alcohol was distilled off to dryness, the
residue was dissolved in 10 mL of water and acidified
with АсОН to рН 6. On cooling the separated crystals
were filtered off, dried, and recrystallized from
aqueous ethanol.
5-Allyl-2,4-dimethyl-1,6-dihydropyrimidin-6-one
1
(1c), mp 151–152°С [7]. H NMR spectrum, δ, ppm:
Crystallographic data of compound 1c are
deposited in the Cambridge Crystallographic Data
Centre (CCDC 1536234).
2.14 s (3Н, СН3), 2.22 (3Н, СН3), 3.13 d.t (2Н, СН2, J
6.0, 1.6 Hz), 4.93 d.d.t (1Н, СН2, J 10.1, 1.8, 1.6 Hz),
4.96 d.d.t (1Н, СН2, J 17.1, 1.8, 1.6 Hz), 5.76 d.d.t
(1Н, СН, J 17.1, 10.1, 6.0 Hz), 12.14 br.s [1Н, NH
(OH)].
5-Substituted 2,4-dimethyl-1,6-dihydropyrimi-
din-6-ones. General procedure. To a solution of
alkali metal ethylate prepared from 0.46 g (0.02 mol)
of metal sodium or potassium and 40 mL of anhydrous
2,4-Dimethyl-5-cyclopentyl-1,6-dihydropyrimi-
din-6-one (1d) was obtained from ethyl 2-cyclopentyl-
RUSSIAN JOURNAL OF ORGANIC CHEMISTRY Vol. 54 No. 5 2018

HARUTYUNYAN et al.
774
3-oxobutanoate. Yield 39%, mp 180–182°С, Rf 0.51
(2-propanol–dichloroethane, 1 : 9), IR spectrum, ν, cm–1:
3290, 3130 (NH), 1850, 1639 (СО), 1610 (C=C–
СНcyclopentyl), 3.36 s (3Н, NСН3), 7.01 d (1Н, С6Н4, J
7.8 Hz), 7.10 t (1Н, С6Н4, J 7.6 Hz), 7.26 s (1Н,
2-СН=C), 7.38 d.d (1Н, С6Н4,1J 7.8, 2J 7.6 Hz), 7.73 d
(1Н, С6Н4, J 7.6 Hz), 14.01 br.s (1Н, NH). Found, %:
C 71.77; H 6.18; N 12.40. C20H21N3O2. Calculated, %:
C 71.62; H 6.31; N 12.53.
1
C=N). H NMR spectrum, δ, ppm: 1.51–1.66 m (4Н),
1.78–2.02 m (4Н) and 2.90–3.02 m (1Н, С5Н9), 2.18 s
(3Н) and 2.19 s (3Н, 2СН3), 11.95 br.s (1Н, NH). 13С
NMR spectrum, δ, ppm: 20.2 (CH3), 21.1 (CH3), 26.0
(2CH3), 28.8 (2CH3), 37.7 (CH), 122.8, 153.9, 158.0,
161.4. Found, %: C 68.89; H 8.51; N 14.65.
C11H16N2O. Calculated, %: C 68.72; H 8.39; N 14.57.
3-[(Z)-1-(5-Benzyl-4-methyl-6-oxo-1,6-dihydro-
pyrimidin-2-yl)methylidene]-1-methylindolin-2-one
(5c) was prepared from 1-methylindoline-2,3-dione
and pyrimidine 1g. Yield 62%, mp 228–230°С, Rf 0.82
(ethanol–dichloroethane, 1 : 1). IR spectrum, ν, cm–1:
2-Substituted pyrimidin-6-ones (5a–5c, 6, 7a–7c)
(general procedure). A mixture of 0.01 mol of 5-sub-
stituted 2,4-dimethyl-1,6-dihydro-6-pyrimidinone,
0.01 mol of N-methylisatin 2, substituted 3-quino-
linealdehyde 3 or cinnamic aldehyde 4, 100 mg of
anhydrous ZnCl2 was heated at 170–180°С for 1 h. On
cooling the product was triturated with ethanol, filtered
off, and dried. The compounds obtained were purified
by recrystallization from alcohol or by hot filtration of
a dispersion of the compound in alcohol. Compounds
5a–5c are red-orange powders, 6, and 7a–7c are
yellow or light yellow powders.
1
1703, 1675 (СО), 1642, 1601 (C=C–C=N). H NMR
spectrum, δ, ppm: 2.31 s (3Н, CH3), 3.36 s (3Н, NCH3),
3.87 s (2Н, CH2), 7.02 br.d (1Н, Н7isatin, J 7.8 Hz), 7.11
t.d (1Н, С6Н4, J 7.8, 0.9 Hz), 7.09–7.16 m (1Н, С6Н5),
7.20–7.23 m (4Н, С6Н5), 7.29 s (1Н, =CH), 7.38 t.d
(1Н, С6Н4, J 7.8, 1.0 Hz), 7.74 br.d (1Н, Н4isatin, J
7.6 Hz), 14.32 br.s (1Н, NH). 13С NMR spectrum, δ,
ppm: 21.0 (СН3), 25.6 (СН3), 30.6 (NСН3), 108.9
(СН), 120.6 (СН), 121.8, 122.6 (СН), 124.8, 125.4
(СН), 127.7 (2СН, Ph), 127.8 (2СН, Ph), 129.6 (СН),
130.9 (СН), 132.2, 149.9, 138.8, 142.5, 150.5, 159.7,
160.7. Found, %: C 74.05; H 5.53; N 11.90.
C22H19N3O2. Calculated, %: C 73.93; H 5.36; N 11.76.
3-[(Z)-1-(5-Butyl-4-methyl-6-oxo-1,6-dihydro-
pyrimidin-2-yl)methylidene]-1-methylindolin-2-one
(5a) was prepared from 1-methylindoline-2,3-dione
and pyrimidine 1a. Yield 60%, mp 243–245°С, Rf 0.75
(ethanol–dichloroethane, 1 : 1). IR spectrum, ν, cm–1:
2-[(Е)-2-(2-Hydroxy-6-methoxyquinol-3-yl)-1-
ethenyl]-4-methyl-5-propyl-1,6-dihydropyrimidin-6-
one (6) was prepared from 6-methoxy-2-chloro-3-
quinolinecarbaldehyde and pyrimidinone 1a. Yield
38%, mp 320°С, Rf 0.67 (isobutanol–Н2О–АсОН,
2 : 2 : 1). IR spectrum, ν, cm–1: 1640 (СО), 1584
1
1701, 1674, 1641 (СО), 1602 (C=C–C=N). H NMR
spectrum, δ, ppm: 0.97 t (3Н, СН3, J 6.9 Hz), 1.35–
1.52 m (4Н, СН2СН2СН3), 2.31 s (3Н, 4-СН3), 2.44–
2.50 m (2Н, 5-СН2СН2), 3.36 s (3Н, NСН3), 7.02 br.d
(1Н, С6Н4, Н7indolinone, J 7.7 Hz), 7.11 t.d (1Н, С6Н4,
Н5indolinone, 1J 7.6, 2J 1.0 Hz), 7.26 s (1Н, 2-СН=C), 7.38
1
(C=C–C=N). H NMR spectrum, δ, ppm: 0.92 t (3Н,
СН3СН2СН2, J 7.3 Hz), 1.39–1.50 m (2Н, СН2СН3),
2.28 s (3Н, СН3), 2.37–2.43 m (2Н, СН2С2Н5), 3.87 s
(3Н, ОСН3), 7.21 d.d (1Н, Н7, С6Н3, J 8.9, 2.8 Hz),
7.27 d (1Н, Н5, С6Н3, J 2.8 Hz), 7.28 d (1Н, Н8, С6Н3,
J 8.9 Hz), 7.57 d [1Н, (E) =CH, J 15.9 Hz], 7.83 d
[1Н, (E) =CH, J 15.9 Hz], 8.17 s (1Н, Н4), 11.96 s
(1Н, ОH), 12.34 br.s (1Н, NH). Found, %: C 68.57; H
5.85; N 11.67. C20H21N3O3. Calculated, %: C 68.36; H
6.02; N 11.96.
1
2
t.d (1Н, С6Н4, Н6indolinone, J 7.7, J 1.0 Hz), 7.73 br.d
(1Н, С6Н4, Н4indolinone, J 7.6 Hz), 14.15 br.s (1Н, NH).
13С NMR spectrum, δ, ppm: 13.5 (СН3), 20.5 (СН3),
22.2 (СН2), 25.2 (СН2), 26.0 (NСН3), 29.7 (СН2),
108.8 (СН), 120.5 (СН), 121.9, 122.6 (СН), 126.4,
129.1 (СН), 130.8 (СН), 131.8, 142.4, 149.9, 158.2,
160.3, 166.4. Found, %: C 70.68; H 6.31; N 12.85.
C19H21N3O2. Calculated, %: C 70.57; H 6.54; N 12.99.
5-Allyl-4-methyl-2-[(1E,3E)-4-phenylbuta-1,3-
dienyl]-1,6-dihydropyrimidin-6-one (7а) was
prepared from (2E,4E)-5-phenylpenta-2,4-dienal and
pyrimidine 1b. Yield 48%, mp 200–202°С, Rf 0.57
(acetone–hexane, 2 : 3). IR spectrum, ν, cm–1: 1649,
3-[(Z)-1-(4-Methyl-6-oxo-5-cyclopentyl-1,6-di-
hydropyrimidin-2-yl)methylidene]-1-methylindolin-
2-one (5b) was prepared from 1-methylindoline-2,3-
dione and pyrimidine 1b. Yield 51%, mp 263–265°С,
Rf 0.78 (ethanol–dichloroethane, 1 : 1). IR spectrum, ν,
1
1625 (СО), 1585 (C=C–C=N). H NMR spectrum, δ,
1
cm–1: 1671, 1641 (СО), 1605 (C=C–C=N). H NMR
ppm: 2.23 s (3H, CH3), 3.18 d.t (2Н, CH2, J 6.2, 1.5 Hz),
4.95 d.q (1Н, =CHH, J 10.0, 1.5 Hz), 5.00 d.q (1H,
=CHH, J 17.1, 1.5 Hz), 5.79 d.d.t (1H, =CH, J 17.1,
spectrum, δ, ppm: 1.56–1.74 m (4Н) and 1.84–2.11 m
[4Н, (СН2)4], 2.35 s (3Н, 4-СН3), 3.00–3.13 m (1Н,
RUSSIAN JOURNAL OF ORGANIC CHEMISTRY Vol. 54 No. 5 2018

SYNTHESIS AND STRUCTURE OF NEW SUBSTITUTED PYRIMIDINONE
775
3,4,5
2, 6
Ph
10.0, 6.2 Hz), 6.32 d [1H, (E)=CH, J 15.2 Hz], 6.86 d
H
P h
), 7.45–7.50 m (2H, H ), 7.59 d.d [1H, (E)=CH,
[1H, (E)=CH, J 15.5 Hz], 6.98 d.d [1H, (E)=CH, J
J 15.3, 10.5 Hz], 12.08 br.s (1H, NH). Found, %: C
78.05; H 7.53; N 9.28. C20H24N2O. Calculated, %: C
77.89; H 7.84; N 9.08.
3,4,5
15.5, 10.5 Hz], 7.20–7.34 m (3H, H ), 7.45–7.50 m
P h
2, 6
Ph
(2H, H ), 7.62 d.d [1H, (E)=CH, J 15.2, 10.5 Hz],
12.20 br.s (1H, NH). Found, %: C 77.83; H 6.47; N
10.30. C18H18N2O. Calculated, %: C 77.67; H 6.52; N
10.06.
ACKNOWLEDGMENTS
The research was performed in the Russian-
Armenian University under the financial support by
the grant from the Russian Ministry of Education and
Science for financing the scientific studies in the
Russian-Armenian University.
5-Butyl-4-methyl-2-[(1E,3E)-4-phenylbuta-1,3-
dienyl]-1,6-dihydropyrimidin-6-one (7b) was
prepared from (2E,4E)-5-phenylpenta-2,4-dienal and
pyrimidine 1c. Yield 59%, mp 184–186°С, Rf 0.61
(acetone–hexane, 2 : 3). IR spectrum, ν, cm–1: 1646,
1
1626 (СО), 1570 (C=C–C=N). H NMR spectrum, δ,
REFERENCES
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CH2CH2Me), 2.23 s (3H, CH3), 2.35–2.44 m (2H,
CH2C3H7), 6.30 d [1H, H1 (E)=CH, J 15.3 Hz], 6.85 d
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J 15.6, 10.6 Hz], 7.20–7.35 m (3H, H ), 7.45–7.50
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7.68; N 9.40. C19H22N2O. Calculated, %: C 77.52; H
7.53; N 9.52.
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1,3-dienyl]-1,6-dihydropyrimidin-6-one (7c) was
prepared from (2E,4E)-5-phenylpenta-2,4-dienal and
pyrimidine 1e. Yield 51%, mp 192–194°С, Rf 0.60
(acetone–hexane, 2 : 3). IR spectrum, ν, cm–1: 1644,
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1
1630 (СО), 1582 (C=C–C=N). H NMR spectrum, δ,
ppm: 0.97 d (6H, 2Me, J 6.6 Hz), 1.26–1.35 m (2H,
CH2CH), 1.62 nonet (1H, CH, J 6.6 Hz), 2.23 s (3H,
CH3), 2.36–2.43 m (2H, CH2CH2CH), 6.30 d [1H, (E)
=CH, J 15.3 Hz], 6.85 d [1H, (E)=CH, J 15.5 Hz], 6.97
d.d [1H, (E)=CH, J 15.5, 10.5 Hz], 7.20–7.34 m (3H,
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p. 786.
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RUSSIAN JOURNAL OF ORGANIC CHEMISTRY Vol. 54 No. 5 2018