18
ERKIN et al.
Table 6. Hydrogen bonds parameters for crystal of
compound 1a
chloride in 3 mL of ethanol was added dropwise at
vigorous stirring to a solution of 0.4 g of thione 3 [11]
and 2 g of sodium hydroxide in 18 mL of water. After
that, the emulsion was slowly heated to 80°С and kept
at that temperature during 1 h. The formed suspension
was cooled down to ambient temperature and filtered.
The precipitate was washed with water, dried under
reduced pressure over phosphorus(V) oxide,
recrystallized from cyclo-hexane (compound 2a),
cyclohexane–ethanol 10 : 1 (compound 2b), or
cyclohexane–ethanol 20 : 3 (compound 2c), washed
with cyclohexane, and dried at 60°С to constant mass.
Bond
Length, d, Å
2.477
Angle, ω, deg
149.8
Cl1C···H−N9A
Cl1C···H−O1B
Cl1C···H−N9C
O1C···H−N9C
Cl1D···H−O1C
2.366
164.2
2.459
157.2
2.041
159.0
2.399
171.7
Cl1E···H−O1C
Cl1E ···H1C−N1C
Cl1E−H1EA···N1C
Cl1D···H−N9E
Cl1E···H−N9A
2.331
2.245
1.893
2.398
2.298
153.8
169.9
175.3
159.6
164.0
ACKNOWLEDGMENTS
Authors are sincerely thankful to V.V. Tets and the
collaborators from Pavlov First St. Petersburg State
Medical University for microbiology experiments.
CONFLICT OF INTERESTS
No conflict of interest was declared by authors.
REFERENCES
using spherical harmonics in the SCALE3 ABSPACK
scaling algorithm implemented in CrysAlisPro
software package. The structure was solved by direct
methods and refined to R1 = 0.043 (wR2 = 0.109) for
14374 independent reflections with |Fo| ≥ 4σF using
SHELX software [9] of OLEX2 package [10].
Positions of the hydrogen atoms were calculated using
the algorithms implemented in SHELX software
package, with Uiso(H) = 1.5Ueq(C) and d(C–H) = 0.96 Å
for CH3 groups, Uiso(H) = 1.2Ueq(C) and d(C–H) = 0.97 Å
for CH2 groups, Uiso(H) = 1.2Ueq(C) and d(C–H) = 0.93 Å
for CH groups of the cyclic fragments, Uiso(H) =
1.2Ueq(C) and d(C–H) = 0.98 Å for tertiary CH groups,
and Uiso(H) = 1.2Ueq(N) and d(N–H) = 0.86 Å for NH2
and NH groups. Positions of hydrogen atoms of the
H2O and HCl molecules were found from the
differential Fourier synthesis and fixed with 1.5Ueq(O)
during refinement. The complete data were deposited
at the Cambridge Crystallographic Data Centre (CCDC
1834763).
1. Geronikaki, A., Fesatidou, M., Kartsev, V., and Maca-
ev, F., Curr. Top. Med. Chem., 2013, vol. 13, no. 21,
p. 2684. doi 10.2174/15680266113136660195
2. Öǧretir, C. and Yaman, M., J. Mol. Struct.
(THEOCHEM), 1999, vol. 458, no. 3, p. 217. doi
10.1016/S0166-1280(98)00070-0
3. Civcir, P.Ü., J. Phys. Org. Chem., 2001, vol. 14, no. 3,
p. 171. doi 10.1002/poc.349
4. Kozlov, A.V., Semenov, V.E., Mikhailov, A.S., Aga-
nov, A.V., Smith, M.B., Reznik, V.S., and Latypov, S.K.,
J. Phys. Chem. B., 2008, vol. 112, no. 10, p. 3259. doi
10.1021/jp710952r
5. Koppel, H.C., Springer, R.H., Robins, R.K., and Cheng, C.C.,
J. Org. Chem., 1961, vol. 26, no. 3, p. 792. doi 10.1021/
jo01062a037
6. The Pyrimidines, Brown, D.J., Evans, F.R., Cowden, W.B.,
and Fenn, M.D., Eds., New York: John Wiley & Sons,
1994, p. 867.
7. Barlin, G.B., Brown, D.J., and Fenn, M.D., Austral. J.
Chem., 1984, vol. 37, no. 11, p. 2391. doi 10.1071/
CH9842391
8. CrysAlisPro, Rigaku Oxford Diffraction, Version
1.171.39.35a, 2017.
9. Sheldrick G.M., Acta Crystallogr. (C)., 2015, vol. 71,
no. 1, p. 3. doi 10.1107/S2053229614024218
10. Dolomanov, O.V., Bourhis, L.J., Gildea, R.J., Ho-
ward, J.A.K., and Pushmann, H., J. Appl. Cryst., 2009,
vol. 42, no. 2, p. 339. doi 10.1107/S0021889808042726
General procedure of synthesis of hydro-
chlorides of 2-amino-4-benzylsulfanyl-6-methylpyri-
midines (1a–1c). Dry hydrogen chloride was vigorously
passed until saturation through a solution (suspension)
of 0.3 g of free base 2a–2c in 15 mL of anhydrous
benzene at room temperature. After removal of the
solvent under reduced pressure or filtration, the residue
was thoroughly washed with hot cyclohexane and
dried at 70°С to constant mass.
General procedure of synthesis of 2-amino-4-
benzylsulfanyl-6-methylpyrimidines (2a–2c). A solu-
tion of equimolar amount of the corresponding benzyl
11. Erkin, A.V., Gurzhii, V.V., and Krutikov, V.I., Russ. J.
Gen. Chem., 2015, vol. 85, no. 1, p. 79. doi 10.1134/
S107036321501014
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 89 No. 1 2019