Pyrimidinophane p-toluenesulfonate-Water-soluble pyrimidine-containing macrocycles

Article abstract of DOI:10.1134/S1070363209010216

Reactions of pyrimidinophanes containing two 6-methylthiocytosine and one 6-methyluracil fragments with methyl p-toluenesulfonate gave amphiphilic macrocyclic bis-p-toluenesulfonates. Despite the presence of several reaction centers in the initial pyrimid

Full text of DOI:10.1134/S1070363209010216

ISSN 1070-3632, Russian Journal of General Chemistry, 2009, Vol. 79, No. 1, pp. 134–137. © Pleiades Publishing, Ltd., 2009.
Original Russian Text © V.E. Semenov, A.S. Mikhailov, E.S. Romanova, A.D. Voloshina, N.V. Kulik, S.Yu. Uraleva, A.V. Kozlov, Sh.K. Latypov, V. S. Reznik,
2009, published in Zhurnal Obshchei Khimii, 2009, Vol. 79, No. 1, pp. 138–141.
Pyrimidinophane p-Toluenesulfonate—
Water-Soluble Pyrimidine-Containing Macrocycles
V. E. Semenov, A. S. Mikhailov, E. S. Romanova, A. D. Voloshina, N. V. Kulik, S. Yu. Uraleva,
A. V. Kozlov, Sh. K. Latypov, and V. S. Reznik
Arbuzov Institute of Organic and Physical Chemistry, Kazan Research Center, Russian Academy of Sciences,
ul. Arbuzova 8, Kazan, 420088 Tatarstan, Russia
e-mail: sve@iopc.knc.ru
Received April 11, 2008
Abstract—Reactions of pyrimidinophanes containing two 6-methylthiocytosine and one 6-methyluracil
fragments with methyl p-toluenesulfonate gave amphiphilic macrocyclic bis-p-toluenesulfonates. Despite the
presence of several reaction centers in the initial pyrimidinophane molecules, methylation occurred only at the
N1 atom (with quaternization) of the 6-methylthiocytosine fragments. Bacteriostatic and fungistatic activity of
the products was estimated.
DOI: 10.1134/S1070363209010216
Macrocyclic compounds containing pyrimidine frag-
ments that are linked to each other through hydro-
carbon bridges are referred to as pyrimidinophanes [1].
These compounds attract interest as potential bio-
logically active substances with a broad spectrum of
action. For example, pyrimidinophanes having bridg-
ing sulfur atoms were reported to exhibit antioxidant
properties [2]. Macrocycles consisting of two 6-methyl-
uracil fragments bridged through methylene chains
incorporating onium moieties showed cholinolytic [3]
and antimicrobial [4] activity.
6-methylpyrimidin-2(1H)-thione] fragments and one
6-methyluracil fragment [5]. In particular, the reaction
of disodium salt II with dibromo derivatives IIIa and
IIIb in DMF gave pyrimidinophanes Ia and Ib
(Scheme 1). In the present work, disodium salt II was
brought into reaction with 1,3-bis(10-bromodecyl)-6-
methyluracil (IIIc) to obtain pyrimidinophane Ic
having decamethylene linkers at the uracil fragment
(Scheme 1).
Pyrimidinophanes Ia–Ic are insoluble in water and
poorly soluble in other polar solvents, such as DMSO.
Poor solubility is a factor hampering testing of these
compounds for biological activity. A common way of
We previously reported on the synthesis of
macrocycles incorporating two thiocytosine [4-amino-
Scheme 1.
NH
NH
(CH2)5
(CH2)nBr (CH2)nBr
NH
NH
N
(CH2)5
4
O
N3
5
6
N
N
N
DMF
3N
N1
2
+
2
H3C
N
S
S
N
CH3
-S
CH3
2Na
1
H3C
N
S-
+
6
4
O
CH3
(CH2)n
(CH2)n
5
O
2'
3'N
N1'
6'
4'
O
CH3
5'
II
IIIa−IIIc
Ia−Ic
I, III, n = 5 (a), 6 (b), 10 (c).
134

PYRIMIDINOPHANE p-TOLUENESULFONATE
135
improving the solubility in polar solvents is introduce-
tion of ammonium, sulfonium, or other onium groups.
However, our attempts to obtain the cor-responding
hydrochlorides by heating pyrim-idinophanes Ia–Ic in
boiling hydrochloric acid, or effect quaternization of
the pyrimidine nitrogen atoms in the 6-methyl-
thiocytosine fragments, or alkylate sulfur atoms therein
by treatment with alkyl bromides were unsuccessful: in
all cases, only the initial pyrimidinophane was isolated
from the reaction mixture.
amphiphilic macrocyclic bis-sulfonates Va–Vc having
onium centers on N1 in the 6-methylthiocytosine
fragments (Scheme 2). The presence of a quaternary
nitrogen atom in the above fragments of macrocycles
Va–Vc is confirmed by considerable downfield shifts
of the 5-H signals and signals from the 4-NHCH2
protons in the H NMR spectra of Va–Vc (CDCl3) as
compared to the corresponding signals in the spectra of
initial pyrimidinophanes Ia–Ic.
1
Amphiphilic pyrimidinophanes Va–Vc are soluble
in both weakly polar (CHCl3) and polar solvents
(water, DMSO). Aqueous solutions of pyrimidino-
phanes Va–Vc were tested for antibacterial activity
against some Gram-positive and Gram-negative bacteria,
as well as some fungi. Compounds Va–Vc turned out
to be selective for Gram-positive Staphylococcus
aureus and Bacillus cereus: the minimal inhibitory
concentrations range from 0.24 to 12.5 μg ml–1, i.e., they
are comparable with the corresponding values for
ciprofloxacin as standard. The antibacterial activity of
pyrimidinophanes increases with rise in the number of
methylene units in the bridging fragments. In tests with
Staphylococcus aureus, the minimal inhibitory con-
centration of compounds Va and Vb was 7.8 μg ml–1,
while the minimal inhibitory concentration of Vc was
0.24 μg ml–1. Pyrimidinophanes Va–Vc showed a
weak or no activity against Gram-negative bacteria and
fungi; the corresponding minimal inhibitory concentra-
tions exceeded 100 μg ml–1.
We succeeded in synthesizing amphiphilic
macrocyclic bis-p-toluenesulfonates Va–Vc by reac-
tion of pyrimidinophanes Ia–Ic with methyl p-to-
luenesulfonate (IV) (Scheme 2). The reactions were
carried out in excess reagent IV which also served as
solvent. Theoretically, the alkylation could involve
both the N1 and N3 atoms in the pyrimidine rings and
nitrogen and sulfur atoms in the bridging fragments.
Using thiocytosine derivatives, namely 4-decylamino-
6-methyl-2-methylsulfanylpyrimidine, 4-dimethylamino-
6-methyl-2-methylsulfanilpyrimidine, and N,N-bis(2-
methylsulfanyl-6-methylpyrimidin-4-yl)hexane-1,6-di-
amine as model compounds we found that their
reactions with ester IV occur exclusively at the N1
atom of the pyrimidine ring to give the corresponding
quaternary salts, 4-decylamino-1,6-dimethyl-2-methyl-
sulfanylpyrimidinium p-toluenesulfonate, 4-dimethyl-
amino-1,6-dimethyl-2-methylsulfanylpyrimidinium p-
toluenesulfonate, and 4,4′-(hexane-1,6-diimino)bis(1,6-
dimethyl-2-methylsulfanylpyrimidinium) bis-p-toluene-
sulfonate [6]. On the basis of these results, elemental
analyses, and NMR spectra the products obtained by
the reactions of pyrimidinophanes Ia–Ic with methyl
p-toluenesulfonate (IV) were assigned the structures of
Thus reactions of pyrimidinophanes Ia–Ic with
methyl p-toluenesulfinate (IV) gave amphiphilic
macrocyclic bis-p-toluenesulfonates Va–Vc as a result
of quaternization of the N1 nitrogen atom in the
thiocytosine fragments. The products are soluble in
Scheme 2.
NH
(CH2)5
NH
N
N
+
O
+
H3C
N
S
S
N
CH3
2
Iа−Ic + CH3OS
CH3
CH3
(CH2)n
H3C
O
(CH2)n
O
SO−
O
CH3
3' N
4'
N 1'
6'
O
2'
O
CH3
5'
IV
V
V, n = 5 (a), 6 (b), 10 (c).
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 79 No. 1 2009

136
SEMENOV et al.
polar solvents, including water, and they showed
bacteriostatic and fungistatic activity.
acetate as eluent. From the latter fraction we isolated
0.6 g (16%) of pyrimidinophane Ic as a thick oil. H
1
NMR spectrum (CDCl3), δ, ppm: 1.28 m (22H, CH2),
1.42 m (4H, CH2), 1.66 m (12H, CH2), 2.22 s (3H, 6′-
CH3), 2.25 s (6H, 6-CH3), 3.06 m (4H, SCH2), 3.33 m
(4H, NHCH2), 3.79 m and 3.90 m (2H each, 1′-CH2,
3′-CH2), 4.84 br.s (2H, NH), 5.55 s (1H, 5′-H), 5.83
(2H, 5-H). Found: m/z 752.4590 [M]+. C40H64N8O2S2.
Calculated: M 752.4593.
EXPERIMENTAL
1
The H NMR spectra were recorded on a Bruker
Avance-600 spectrometer using tetramethylsilane as
internal reference. The electron-impact mass spectrum
(70 eV) was obtained on a Finnigan MAT-212 mass
spectrometer at a resolution of 1000. The melting
points were determined on a Boetius melting point
apparatus and are uncorrected. Thin-layer chromato-
graphy was performed on Silufol UV-254 plates; spots
were visualized under UV light. Aluminum oxide of
Brockmann activity grade II was used for column
chromatography.
11,12,21,32,33-Pentamethyl-23,37-dioxo-14,30-
dithia-2,8,20,24,35,36-hexaaza-12,32-diazoniatetra-
cyclo[29.3.1.19,13.120,24]heptatriaconta-1(35),9(36),10,
12,21,31,33-heptaene bis(p-toluenesulfonate) (Va). A
mixture of 100 mg of pyrimidinophane Ia and 0.6 g of
methyl p-toluenesulfonate (IV) was stirred for 7 h at
90–100°C. The mixture was cooled to room
temperature, 25 ml of diethyl ether was added, and the
liquid phase was separated from the precipitate by
decanting. This procedure was repeated five times, and
the crystalline product was dried under reduced
pressure (0.1 mm). Yield 0.14 g (89%), mp 67–69°C.
1H NMR spectrum (CDCl3), δ, ppm (J, Hz): 1.47 m
(4H, CH2), 1.62 m (6H, CH2), 1.76 m (8H, CH2), 2.20
s (3H, 6′-CH3), 2.34 br.s (12H, 6-CH3, C6H4CH3), 3.11
m (4H, SCH2), 3.62 m (10H, NHCH2, N+CH3), 3.74 m
and 3.88 m (2H each, 1′-CH2, 3′-CH2), 5.55 s (1H, 5′-
H), 6.71 (1H, 5-H), 6.73 (1H, 5-H), 7.15 d (4H, C6H4,
3J = 7.8), 7.75 d (4H, C6H4, 3J = 8.1), 9.42 s and 9.46 s
(1H each, NH). Found, %: C 56.20; H 6.48; N 11.48; S
13.19. C46H64N8O8S4. Calculated, %: C 56.07; H 6.55;
N 11.37; S 13.02.
Disodium
N,N′-(pentane-1,5-diyl)bis(4-amino-6-
methylpyrimidine-2-thiolate) (II) [7], 1,3-bis(5-
bromopentyl)-6-methyluracil (IIIa) [8], and 1,3-bis(6-
bromohexyl)-6-methyluracil (IIIb) [4] were synthe-
sized according to known procedures. Methyl p-toluene-
sulfonate (IV) was commercial product.
1,3-Bis(10-bromodecyl)-6-methylpyrimidin-2,4
(1H,3H)-dione (IIIc). 1,10-Dibromodecane, 51 g, was
added under stirring at room temperature to a
suspension of 9.6 g of 6-methyluracil disodium salt [8]
in 100 ml of dimethylformamide. The mixture was
stirred for 15 h at 60–70°C, the solvent was distilled
off, the residue was treated with 50 ml of acetone, and
the mixture was filtered. The filtrate was concentrated
and subjected to column chromatography on aluminum
oxide using (in succession) petroleum ether and
petroleum ether–diethyl ether (5:1) as eluent. From the
second fraction we isolated 6.4 g (40%) of compound
11,12,22,34,35-Pentamethyl-24,39-dioxo-14,32-
dithia-2,8,21,25,37,38-hexaaza-12,34-diazoniatetra-
cyclo[31.3.1.19,13.121,25]nonatriaconta-1(37),9(38),10,
12,22,33,35-heptaene bis(p-toluenesulfonate) (Vb)
was synthesized in a similar way from 0.1 g of pyrim-
idinophane Ib and 0.6 g of ester IV. Yield 0.14 g
1
IIIc as an oily substance. H NMR spectrum (CDCl3),
δ, ppm (J, Hz): 1.34 m (24H, CH2), 1.60 m (4H, CH2),
1.82 m (4H, CH2), 2.21 s (3H, 6-CH3), 3.37 m (4H,
3
1
CH2Br), 3.77 t (2H, NCH2, J = 8.1), 3.88 t (2H,
(92%), mp 67–69°C. H NMR spectrum (CDCl3), δ,
NCH2, 3J = 7.7), 5.59 s (1H, 5-H). Found, %: C 53.30;
H 7.94; Br 28.18; N 5.10. C25H44Br2N2O2. Calculated,
%: C 53.20; H 7.86; Br 28.31; N 4.96.
ppm (J, Hz): 1.47 m (4H, CH2), 1.62 m (6H, CH2),
1.76 m (8H, CH2), 2.09 m (4H, CH2), 2.22 s (3H, 6′-
CH3), 2.34 br.s (12H, 6-CH3, C6H4CH3), 3.14 m (4H,
SCH2), 3.62 m (10H, NHCH2, N+CH3), 3.74 m and
3.88 m (2H each, 1′-CH2, 3′-CH2), 5.55 s (1H, 5′-H),
6.73 (1H, 5-H), 6.76 (1H, 5-H), 7.16 d (4H, C6H4, 3J =
7.9), 7.79 d (4H, C6H4, 3J = 7.9), 9.53 s and 9.57 s (1H
each, NH). Found, %: C 56.80; H 6.60; N 11.19; S
12.40. C48H68N8O8S4. Calculated, %: C 56.89; H 6.76;
N 11.06; S 12.66.
11,26,43-Trimethyl-14,40-dithia-2,8,12,25,29,42,
45,46-octaazatetracyclo[39.3.1.19,13.125,29]heptatetra-
conta-1(45),9(46),10,12,26,41,43-heptaene-28,47-
dione (Ic). A mixture of 2.1 g of disodium salt II and
3.0 g of compound IIIc in 1000 ml of DMF was stirred
for 7 h at room temperature. The solvent was removed
under reduced pressure, and the residue was subjected
to column chromatography on Al2O3 using (in
succession) petroleum ether, diethyl ether, and ethyl
11,12,26,42,43-Pentamethyl-28,47-dioxo-14,40-di-
thia-2,8,25,29,45,46-hexaaza-12,42-diazoniatetra-
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 79 No. 1 2009

PYRIMIDINOPHANE p-TOLUENESULFONATE
137
cyclo[39.3.1.19,13.125,29]heptatetraconta-1(45),9(46),
10,12,26,41,43-heptaene bis(p-toluenesulfonate) (Vc)
was synthesized in a similar way from 0.1 g of
pyrimidinophane (Ic) and 0.6 g of ester IV. Yield 0.14 g
thanks the Foundation for Support of the Russian
Science for financial support.
REFERENCES
1
(96%), oily substance. H NMR spectrum (CDCl3), δ,
1. Itahara, T., Bull. Chem. Soc. Jpn., 1996, vol. 69, no. 11,
ppm (J, Hz): 1.30 m (24H, CH2), 1.62–1.72 m (14H,
CH2), 2.23 s (3H, 6′-CH3), 2.33 s and 2.35 s (6H each,
6-CH3, C6H4CH3), 3.03 m (4H, SCH2), 3.60 m (10H,
NHCH2, N+CH3), 3.81 m and 3.91 m (2H each, 1′-
CH2, 3′-CH2), 5.57 s (1H, 5′-H), 6.78 (2H, 5-H), 7.14 d
(4H, C6H4, 3J = 9.8), 7.75 d (4H, C6H4, 3J = 9.8), 9.42 s
and 9.37 br. s (1H each, NH). Found, %: C 59.60; H
7.40; N 9.90; S 11.21. C56H84N8O8S4. Calculated, %: C
59.76; H 7.52; N 9.96; S 11.40.
p. 3239.
2. Krivonogov, V.P., Tolstikov, G.A., Kozlova, G.G.,
Sivkova, G.A., Lazareva, D.N., Murinov, Yu.I., Zaru-
dii, F.S., Myshkin, V.A., Ismagilova, A.F., Spirikhin, L.V.,
and Abdrakhmanov, I.B., Proc. I Int. Conf. on the
Chemistry and Biological Activity of Nitrogen-Containing
Heterocycles and Alkaloids, Moscow: Iridium, 2001, vol. 1,
p. 3483.
3. Zobov, VV., Petrov, K.A., Semenov, V.E., Giniyatul-
lin, R.Kh., Nikolaev, A.E., Akamsin, V.D., Galyamet-
dinova, I.V., Nafikova, A.A., Ismaev, I.E., Kataev, V.E.,
Latypov, Sh.K., and Reznik, V.S., Sovr. Probl. Toksikol.,
2006, no. 2, p. 13.
4. Semenov, V.E., Voloshina, A.D., Toroptzova, E.M., Ku-
lik, N.V., Zobov, V.V., Giniyatullin, R.Kh., Mikhailov, A.S.,
Nikolaev, A.E., Akamsin, V.D., and Reznik, V.S., Eur. J.
Med. Chem., 2006, vol. 41, no. 9, p.1093.
5. Mikhailov, A.S., Giniyatullin, R.Kh., Semenov, V.E.,
Reznik, V.S., Nafikova, A.A., Latypov, Sh.K., Efre-
mov, Yu.Ya., and Sharafutdinova, D.R., Izv. Ross. Akad.
Nauk, Ser. Khim., 2003, no. 6, p. 1324.
The antimicrobial activity of compounds Va–Vc
was estimated by the double serial dilution technique
[9] in a liquid nutrient with respect to bacteria strains
Pseudomonas aeruginosa 9027, Escherichia coli F-50,
Staphylococcus aureus 209p and Bacillus cereus 8035
and fungi Aspergillus niger BKMF-1119 and
Trichophyton mentagrophytes var. gypseum 1773. The
minimal inhibitory concentration was determined as
the lowest concentration of a substance under study,
which retained growth of the corresponding test
microorganism. Growth of bacteria or fungi or the
absence of growth (due to bacteriostatic or fungistatic
effect of the given compound) was observed.
6. Kozlov, A., Semenov, V., Mikhailov, A., Aganov, A.,
Smith, M., Reznik, V., and Latypov, S., J. Phys. Chem. B,
2008, vol. 112, no. 10, p. 3259.
7. Mikhailov, A.S., Skuzlova, V.I., Pashkurov, N.G., and
Reznik, V.S., Russ. J. Gen. Chem., 1996, vol. 66, no. 2,
p. 500.
ACKNOWLEDGMENTS
This study was performed under financial support
by the Russian Foundation for Basic Research (project
no. 07-03-00392-a), by program no. 8 of the Presidium
of the Russian Academy of Sciences, and by program
no. 10 of the Department of Chemistry and Materials
Science, Russian Academy of Sciences. Sh.K. Latypov
8. Reznik, V.S., Salikhov, I.Sh., Shvetsov, Yu.S., and Iva-
nov, .E., Izv. Akad. Nauk SSSR, Ser. Khim., 1980, no. 11,
p. 2568.
9. Pershin, G.N., Metody eksperimental’noi khimioterapii
(Methods of Experimental Chemotherapy), Moscow:
Meditsinskaya Literatura, 1971, pp. 100, 109.
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