supplementary materials


tk5215 scheme

Acta Cryst. (2013). E69, o698    [ doi:10.1107/S1600536813009537 ]

N-Benzylthieno[3,2-d]pyrimidin-4-amine

P. Starha and Z. Trávnícek

Abstract top

The title compound, C13H11N3S, crystallizes with two independent molecules in the asymmetric unit. The two molecules are geometrically very similar and differ mainly in a spatial orientation of the benzene and thieno[3,2-d]pyrimidine ring systems [dihedral angles = 69.49 (4) and 79.05 (3)°]. The nine-membered thieno[3,2-d]pyrimidine moieties have a planar conformation (r.m.s. deviations = 0.020 and 0.012 Å). In the crystal, molecules are linked through N-H...N, N-H...C and C-H...[pi] non-covalent contacts into chains along the c axis, while neighbouring chains are connected via C-H...N interactions.

Comment top

The essentially planar thieno[3,2-d]pyrimidine moiety is formed by six-membered (pyrimidine) and five-membered (thiophene) rings, which form a dihedral angle of 2.53 (4)° and 1.24 (4)° (for the molecule with the N1 and N1A atoms, respectively). The thieno[3,2-d]pyrimidine moiety is substituted by benzylamine at the C4 position (Fig. 1). The dihedral angles formed by the benzene and thieno[3,2-d]pyrimidine rings is 69.49 (4)° for the N1-molecule, and 79.05 (3)° for the N1A-molecule. The N4—H4···N1i (for the molecule with the N1 atom) and N4A—H4A···N1Aii (for the molecule with the N1A atom) hydrogen bonds together with other non-covalent contacts of the type N—H···C and C—H···π (Fig. 2, Table 1) connect the individual molecules into chains along the c axis (symmetry codes: i) x, –y+0.5, z+0.5; ii) x, –y+1.5, z–0.5). The neighbouring chains are connected through the C15–H15···N3A and and C2A—H2A···N3 interactions.

Related literature top

For the synthesis of 4-benzylaminothieno[3,2-d]pyrimidine hydrochloride, its NMR characterization (DMSO-d6 solution) and biological activity, see: Crespo et al. (1998).

Experimental top

4-Chlorothieno[3,2-d]pyrimidine (10.0 mmol) was dissolved in 50 ml of 2-propanol. Benzylamine (13.0 mmol) and triethylamine (16.0 mmol) were subsequently added to the reaction mixture, which was stirred at 60 °C. The TLC control showed one spot after 18 h. After that, the mixture was evaporated and suspended in distilled water (20 ml). The product was collected by filtration, washed with distilled water and 2-propanol and dried in a desiccator over silica gel. Part of the product was recrystallized from acetone, which led to a crystalline product containing the crystals suitable for a single-crystal X-ray analysis. 1H NMR (DMF-d7, TMS, 298 K, p.p.m.): δ 8.52 (s, 1H, HC2), 8.41 (t, J = 6.5 Hz, 1H, HN4), 8.14 (d, J = 5.3 Hz, 1H, HC6), 7.44 (d, J = 7.7 Hz, 2H, HC11,15), 7.42 (d, J = 5.5 Hz, 1H, HC7), 7.33 (t, J = 7.7 Hz, 2H, HC12,14), 7.25 (t, J = 7.5 Hz, 1H, HC13), 4.87 (d, J = 6.0 Hz, 2H, HC9). 13C NMR (DMF-d7, TMS, 298 K, p.p.m.): δ 160.6 (C7`), 158.0 (C4), 155.4 (C2), 140.6 (C10), 133.2 (C6), 129.0 (C12,14), 128.2 (C11,15), 127.5 (C13), 125.4 (C7), 115.8 (C4`), 44.5 (C9). Analysis calculated for C13H11N3S1: C 64.7, H 4.6, N 17.4, S 13.3%; found: C 64.3, H 4.6, N 17.3, S 12.8%. Elemental analysis (C, H, N) was performed on a Thermo Scientific Flash 2000 CHNO-S Analyzer. The 1H and 13C NMR spectra (DMF-d7 solutions, calibrated against tetramethylsilane) were collected at 298 K on a Varian 400 spectrometer at 400.00 and 100.58 MHz, respectively.

Refinement top

Non-hydrogen atoms were refined anisotropically and hydrogen atoms were located in difference maps and refined using the riding model with C—H = 0.95 (CH), C—H = 0.99 (CH2) Å, and N—H = 0.88 Å, with Uiso(H) = 1.2Ueq(CH, CH2, NH).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2011); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. Two crystallographically independent molecules of the title compound with the non-hydrogen atoms depicted with anisotropic displacement ellipsoids at the 50% probability level and given with the atom numbering scheme.
[Figure 2] Fig. 2. Part of the crystal structure, showing the formation of one-dimensional chains as well as non-covalent ineteractions within (N4—H4···N1 hydrogen bond (dashed green lines) and C7—H7···π, N4A—H4A···C2A (dashed orange lines)) and between (C15–H15···N3A and C2A—H2A···N3; dashed orange lines; see Table 1 for parameters) the chains.
N-Benzylthieno[3,2-d]pyrimidin-4-amine top
Crystal data top
C13H11N3SF(000) = 1008
Mr = 241.31Dx = 1.370 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 15514 reflections
a = 19.3430 (4) Åθ = 3.0–33.2°
b = 9.46296 (16) ŵ = 0.26 mm1
c = 12.8221 (2) ÅT = 120 K
β = 94.3231 (17)°Prism, colourless
V = 2340.30 (7) Å30.40 × 0.40 × 0.25 mm
Z = 8
Data collection top
Agilent Xcalibur Sapphire2
diffractometer
4109 independent reflections
Radiation source: Enhance (Mo) X-ray Source3528 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
Detector resolution: 8.3611 pixels mm-1θmax = 25.0°, θmin = 3.0°
ω scansh = 2323
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)
k = 1111
Tmin = 0.905, Tmax = 0.939l = 1515
19406 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.029Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.078H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0476P)2 + 0.4186P]
where P = (Fo2 + 2Fc2)/3
4109 reflections(Δ/σ)max < 0.001
307 parametersΔρmax = 0.28 e Å3
0 restraintsΔρmin = 0.25 e Å3
Crystal data top
C13H11N3SV = 2340.30 (7) Å3
Mr = 241.31Z = 8
Monoclinic, P21/cMo Kα radiation
a = 19.3430 (4) ŵ = 0.26 mm1
b = 9.46296 (16) ÅT = 120 K
c = 12.8221 (2) Å0.40 × 0.40 × 0.25 mm
β = 94.3231 (17)°
Data collection top
Agilent Xcalibur Sapphire2
diffractometer
4109 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)
3528 reflections with I > 2σ(I)
Tmin = 0.905, Tmax = 0.939Rint = 0.019
19406 measured reflectionsθmax = 25.0°
Refinement top
R[F2 > 2σ(F2)] = 0.029H-atom parameters constrained
wR(F2) = 0.078Δρmax = 0.28 e Å3
S = 1.07Δρmin = 0.25 e Å3
4109 reflectionsAbsolute structure: ?
307 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S50.108822 (18)0.10694 (4)0.60102 (3)0.02112 (11)
S5A0.45872 (2)0.62119 (4)0.66155 (3)0.03086 (12)
N3A0.31415 (6)0.88825 (12)0.75775 (9)0.0224 (3)
N30.19707 (6)0.41535 (12)0.44021 (8)0.0206 (3)
C2A0.33340 (8)0.87296 (15)0.85980 (11)0.0248 (3)
H2A0.30660.92410.90620.030*
C20.19194 (7)0.34543 (15)0.34913 (10)0.0223 (3)
H20.20920.39420.29170.027*
N1A0.38455 (6)0.79651 (13)0.90461 (9)0.0271 (3)
N10.16633 (6)0.21820 (12)0.32771 (8)0.0222 (3)
C7A'0.42113 (7)0.72184 (14)0.83595 (11)0.0227 (3)
C7'0.14191 (7)0.15142 (14)0.41194 (10)0.0186 (3)
C4A'0.40431 (7)0.72635 (14)0.72891 (11)0.0204 (3)
C4'0.14582 (7)0.21307 (14)0.51077 (10)0.0174 (3)
N40.18145 (6)0.41308 (12)0.61780 (8)0.0198 (3)
H40.17500.36220.67370.024*
N4A0.33088 (6)0.82477 (13)0.58732 (9)0.0238 (3)
H4A0.35040.76730.54430.029*
C40.17530 (6)0.34889 (14)0.52409 (10)0.0170 (3)
C4A0.34922 (7)0.81394 (14)0.68957 (10)0.0193 (3)
C7A0.47914 (8)0.63230 (16)0.86262 (13)0.0323 (4)
H7A0.49820.61650.93210.039*
C70.10891 (7)0.01643 (15)0.41142 (10)0.0221 (3)
H70.10170.04150.35110.026*
C6A0.50344 (8)0.57307 (18)0.77755 (13)0.0373 (4)
H6A0.54190.51030.78090.045*
C60.08920 (7)0.01926 (15)0.50635 (11)0.0232 (3)
H60.06660.10580.51990.028*
C90.19815 (7)0.56162 (15)0.63204 (11)0.0232 (3)
H9A0.21320.60070.56580.028*
H9B0.23710.57160.68620.028*
C9A0.28012 (7)0.92695 (16)0.54290 (11)0.0275 (3)
H9D0.24340.94030.59170.033*
H9C0.25810.88940.47640.033*
C10A0.31332 (7)1.06765 (16)0.52284 (11)0.0264 (3)
C100.13638 (7)0.64490 (14)0.66460 (10)0.0194 (3)
C110.06933 (7)0.60827 (14)0.62788 (11)0.0227 (3)
H110.06220.53330.57900.027*
C11A0.32231 (7)1.16842 (17)0.60148 (12)0.0297 (3)
H11A0.30501.15080.66760.036*
C12A0.35621 (8)1.29412 (17)0.58469 (13)0.0344 (4)
H12A0.36181.36240.63900.041*
C120.01270 (8)0.68002 (15)0.66191 (12)0.0285 (3)
H120.03290.65380.63640.034*
C130.02237 (8)0.78964 (15)0.73294 (12)0.0291 (3)
H130.01640.83800.75700.035*
C13A0.38197 (8)1.32031 (18)0.48879 (13)0.0360 (4)
H13A0.40611.40570.47760.043*
C140.08889 (8)0.82823 (15)0.76859 (11)0.0265 (3)
H140.09590.90420.81670.032*
C14A0.37252 (9)1.22257 (19)0.40976 (13)0.0388 (4)
H14A0.38951.24120.34350.047*
C15A0.33837 (8)1.09711 (18)0.42644 (12)0.0328 (4)
H15A0.33201.03020.37130.039*
C150.14548 (7)0.75657 (14)0.73447 (11)0.0228 (3)
H150.19100.78420.75920.027*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S50.0280 (2)0.01963 (19)0.01620 (18)0.00222 (13)0.00445 (14)0.00056 (13)
S5A0.0272 (2)0.0318 (2)0.0339 (2)0.00627 (15)0.00492 (16)0.00622 (16)
N3A0.0211 (6)0.0247 (6)0.0218 (6)0.0000 (5)0.0039 (5)0.0010 (5)
N30.0206 (6)0.0243 (6)0.0169 (6)0.0002 (5)0.0024 (5)0.0031 (5)
C2A0.0263 (8)0.0272 (8)0.0217 (7)0.0011 (6)0.0061 (6)0.0019 (6)
C20.0221 (7)0.0294 (8)0.0158 (7)0.0000 (6)0.0033 (5)0.0041 (6)
N1A0.0291 (7)0.0310 (7)0.0212 (6)0.0007 (5)0.0017 (5)0.0004 (5)
N10.0233 (6)0.0271 (7)0.0163 (6)0.0019 (5)0.0027 (5)0.0012 (5)
C7A'0.0219 (7)0.0210 (7)0.0252 (7)0.0047 (5)0.0004 (6)0.0020 (6)
C7'0.0168 (7)0.0225 (7)0.0165 (7)0.0055 (5)0.0012 (5)0.0008 (5)
C4A'0.0185 (7)0.0186 (7)0.0244 (7)0.0039 (5)0.0046 (5)0.0011 (6)
C4'0.0162 (7)0.0198 (7)0.0163 (6)0.0048 (5)0.0018 (5)0.0018 (5)
N40.0260 (6)0.0182 (6)0.0155 (6)0.0013 (5)0.0037 (5)0.0004 (5)
N4A0.0262 (6)0.0262 (7)0.0191 (6)0.0014 (5)0.0020 (5)0.0008 (5)
C40.0137 (6)0.0205 (7)0.0168 (7)0.0047 (5)0.0010 (5)0.0014 (5)
C4A0.0176 (7)0.0198 (7)0.0206 (7)0.0062 (5)0.0029 (5)0.0000 (6)
C7A0.0294 (8)0.0327 (9)0.0334 (9)0.0006 (7)0.0069 (7)0.0046 (7)
C70.0253 (7)0.0220 (7)0.0186 (7)0.0034 (6)0.0009 (6)0.0042 (6)
C6A0.0272 (9)0.0331 (9)0.0505 (11)0.0095 (7)0.0028 (7)0.0015 (8)
C60.0257 (8)0.0191 (7)0.0247 (7)0.0002 (6)0.0003 (6)0.0014 (6)
C90.0240 (8)0.0222 (7)0.0239 (7)0.0042 (6)0.0050 (6)0.0033 (6)
C9A0.0221 (8)0.0361 (9)0.0237 (7)0.0012 (6)0.0027 (6)0.0028 (6)
C10A0.0176 (7)0.0332 (8)0.0280 (8)0.0066 (6)0.0013 (6)0.0080 (7)
C100.0238 (7)0.0174 (7)0.0173 (7)0.0019 (5)0.0033 (5)0.0040 (5)
C110.0281 (8)0.0181 (7)0.0213 (7)0.0005 (6)0.0015 (6)0.0008 (6)
C11A0.0234 (8)0.0353 (9)0.0307 (8)0.0056 (6)0.0036 (6)0.0045 (7)
C12A0.0296 (9)0.0320 (9)0.0413 (10)0.0048 (7)0.0009 (7)0.0031 (7)
C120.0239 (8)0.0245 (8)0.0367 (9)0.0009 (6)0.0007 (6)0.0057 (7)
C130.0315 (9)0.0209 (8)0.0360 (8)0.0064 (6)0.0105 (7)0.0058 (6)
C13A0.0299 (9)0.0316 (9)0.0465 (10)0.0038 (7)0.0026 (7)0.0133 (8)
C140.0398 (9)0.0161 (7)0.0245 (8)0.0010 (6)0.0078 (6)0.0002 (6)
C14A0.0365 (9)0.0459 (10)0.0344 (9)0.0039 (8)0.0050 (7)0.0172 (8)
C15A0.0330 (9)0.0384 (9)0.0266 (8)0.0055 (7)0.0000 (7)0.0067 (7)
C150.0275 (8)0.0190 (7)0.0218 (7)0.0055 (6)0.0025 (6)0.0016 (6)
Geometric parameters (Å, º) top
S5—C61.7246 (14)C6A—H6A0.9500
S5—C4'1.7277 (13)C6—H60.9500
S5A—C6A1.7245 (17)C9—C101.5159 (19)
S5A—C4A'1.7266 (14)C9—H9A0.9900
N3A—C2A1.3410 (19)C9—H9B0.9900
N3A—C4A1.3447 (18)C9A—C10A1.509 (2)
N3—C21.3395 (18)C9A—H9D0.9900
N3—C41.3408 (17)C9A—H9C0.9900
C2A—N1A1.3216 (19)C10A—C11A1.389 (2)
C2A—H2A0.9500C10A—C15A1.389 (2)
C2—N11.3228 (19)C10—C151.3880 (19)
C2—H20.9500C10—C111.390 (2)
N1A—C7A'1.3671 (19)C11—C121.387 (2)
N1—C7'1.3660 (17)C11—H110.9500
C7A'—C4A'1.387 (2)C11A—C12A1.383 (2)
C7A'—C7A1.427 (2)C11A—H11A0.9500
C7'—C4'1.3918 (18)C12A—C13A1.383 (2)
C7'—C71.428 (2)C12A—H12A0.9500
C4A'—C4A1.4127 (19)C12—C131.384 (2)
C4'—C41.4112 (19)C12—H120.9500
N4—C41.3436 (17)C13—C141.382 (2)
N4—C91.4507 (18)C13—H130.9500
N4—H40.8800C13A—C14A1.374 (2)
N4A—C4A1.3361 (17)C13A—H13A0.9500
N4A—C9A1.4626 (18)C14—C151.386 (2)
N4A—H4A0.8800C14—H140.9500
C7A—C6A1.342 (2)C14A—C15A1.383 (2)
C7A—H7A0.9500C14A—H14A0.9500
C7—C61.3457 (19)C15A—H15A0.9500
C7—H70.9500C15—H150.9500
C6—S5—C4'90.65 (6)N4—C9—C10111.45 (11)
C6A—S5A—C4A'90.33 (7)N4—C9—H9A109.3
C2A—N3A—C4A117.47 (12)C10—C9—H9A109.3
C2—N3—C4117.42 (12)N4—C9—H9B109.3
N1A—C2A—N3A128.83 (13)C10—C9—H9B109.3
N1A—C2A—H2A115.6H9A—C9—H9B108.0
N3A—C2A—H2A115.6N4A—C9A—C10A111.58 (11)
N1—C2—N3129.24 (13)N4A—C9A—H9D109.3
N1—C2—H2115.4C10A—C9A—H9D109.3
N3—C2—H2115.4N4A—C9A—H9C109.3
C2A—N1A—C7A'114.19 (12)C10A—C9A—H9C109.3
C2—N1—C7'113.79 (11)H9D—C9A—H9C108.0
N1A—C7A'—C4A'121.81 (13)C11A—C10A—C15A118.36 (15)
N1A—C7A'—C7A126.04 (13)C11A—C10A—C9A120.90 (13)
C4A'—C7A'—C7A112.15 (13)C15A—C10A—C9A120.68 (14)
N1—C7'—C4'121.84 (13)C15—C10—C11118.57 (13)
N1—C7'—C7126.25 (12)C15—C10—C9120.62 (12)
C4'—C7'—C7111.89 (12)C11—C10—C9120.78 (12)
C7A'—C4A'—C4A119.06 (12)C12—C11—C10120.68 (13)
C7A'—C4A'—S5A111.77 (11)C12—C11—H11119.7
C4A—C4A'—S5A129.15 (11)C10—C11—H11119.7
C7'—C4'—C4119.06 (12)C12A—C11A—C10A120.81 (14)
C7'—C4'—S5111.67 (10)C12A—C11A—H11A119.6
C4—C4'—S5129.22 (10)C10A—C11A—H11A119.6
C4—N4—C9123.67 (11)C11A—C12A—C13A119.95 (16)
C4—N4—H4118.2C11A—C12A—H12A120.0
C9—N4—H4118.2C13A—C12A—H12A120.0
C4A—N4A—C9A123.62 (12)C13—C12—C11120.22 (14)
C4A—N4A—H4A118.2C13—C12—H12119.9
C9A—N4A—H4A118.2C11—C12—H12119.9
N3—C4—N4119.55 (12)C14—C13—C12119.49 (14)
N3—C4—C4'118.59 (12)C14—C13—H13120.3
N4—C4—C4'121.85 (12)C12—C13—H13120.3
N4A—C4A—N3A119.21 (12)C14A—C13A—C12A119.88 (16)
N4A—C4A—C4A'122.19 (12)C14A—C13A—H13A120.1
N3A—C4A—C4A'118.60 (12)C12A—C13A—H13A120.1
C6A—C7A—C7A'111.74 (14)C13—C14—C15120.26 (14)
C6A—C7A—H7A124.1C13—C14—H14119.9
C7A'—C7A—H7A124.1C15—C14—H14119.9
C6—C7—C7'112.17 (12)C13A—C14A—C15A120.15 (16)
C6—C7—H7123.9C13A—C14A—H14A119.9
C7'—C7—H7123.9C15A—C14A—H14A119.9
C7A—C6A—S5A114.02 (12)C14A—C15A—C10A120.83 (16)
C7A—C6A—H6A123.0C14A—C15A—H15A119.6
S5A—C6A—H6A123.0C10A—C15A—H15A119.6
C7—C6—S5113.61 (11)C14—C15—C10120.76 (13)
C7—C6—H6123.2C14—C15—H15119.6
S5—C6—H6123.2C10—C15—H15119.6
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C10–C15 ring.
D—H···AD—HH···AD···AD—H···A
N4—H4···N1i0.882.132.999 (2)167
N4A—H4A···N1Aii0.882.052.872 (2)156
C7—H7···Cgiii0.952.583.5317 (13)175
C2A—H2A···N3iv0.952.673.527 (2)150
C15—H15···N3A0.952.583.4842 (18)159
Symmetry codes: (i) x, y+1/2, z+1/2; (ii) x, y+3/2, z1/2; (iii) x, y+1/2, z1/2; (iv) x, y+3/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C10–C15 ring.
D—H···AD—HH···AD···AD—H···A
N4—H4···N1i0.882.132.999 (2)167
N4A—H4A···N1Aii0.882.052.872 (2)156
C7—H7···Cgiii0.952.583.5317 (13)175
C2A—H2A···N3iv0.952.673.527 (2)150
C15—H15···N3A0.952.583.4842 (18)159
Symmetry codes: (i) x, y+1/2, z+1/2; (ii) x, y+3/2, z1/2; (iii) x, y+1/2, z1/2; (iv) x, y+3/2, z+1/2.
Acknowledgements top

This work was supported by Palacký University (grant No. PrF_2013_015). The authors wish to thank Dr Igor Popa for performingthe NMR spectroscopy and Mr Tomáš Šilha for performing CHN elemental analysis.

references
References top

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