N-Benzyl-thieno[3,2-d]pyrimidin-4-amine.

The title compound, C13H11N3S, crystallizes with two independent mol-ecules in the asymmetric unit. The two mol-ecules 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, mol-ecules are linked through N-H⋯N, N-H⋯C and C-H⋯π non-covalent contacts into chains along the c axis, while neighbouring chains are connected via C-H⋯N inter-actions.

Related literature

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

Experimental

Crystal data

C13H11N3S

M = 241.31

Monoclinic,

a = 19.3430 (4) Å

b = 9.46296 (16) Å

c = 12.8221 (2) Å

β = 94.3231 (17)°

V = 2340.30 (7) Å3

Z = 8

Mo Kα radiation

μ = 0.26 mm−1

T = 120 K

0.40 × 0.40 × 0.25 mm

Data collection

Agilent Xcalibur Sapphire2 diffractometer

Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012 ▶) T min = 0.905, T max = 0.939

19406 measured reflections

4109 independent reflections

3528 reflections with I > 2σ(I)

R int = 0.019

Refinement

R[F 2 > 2σ(F 2)] = 0.029

wR(F 2) = 0.078

S = 1.07

4109 reflections

307 parameters

H-atom parameters constrained

Δρmax = 0.28 e Å−3

Δρmin = −0.25 e Å−3

Data collection: CrysAlis PRO (Agilent, 2012 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; 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 ▶).

Click here for additional data file.

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536813009537/tk5215sup1.cif

Click here for additional data file.

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813009537/tk5215Isup2.hkl

Click here for additional data file.

Supplementary material file. DOI: 10.1107/S1600536813009537/tk5215Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C13H11N3S	F(000) = 1008
Mr = 241.31	Dx = 1.370 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 15514 reflections
a = 19.3430 (4) Å	θ = 3.0–33.2°
b = 9.46296 (16) Å	µ = 0.26 mm−1
c = 12.8221 (2) Å	T = 120 K
β = 94.3231 (17)°	Prism, colourless
V = 2340.30 (7) Å3	0.40 × 0.40 × 0.25 mm
Z = 8

Agilent Xcalibur Sapphire2 diffractometer	4109 independent reflections
Radiation source: Enhance (Mo) X-ray Source	3528 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.019
Detector resolution: 8.3611 pixels mm-1	θmax = 25.0°, θmin = 3.0°
ω scans	h = −23→23
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012)	k = −11→11
Tmin = 0.905, Tmax = 0.939	l = −15→15
19406 measured reflections

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.029	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.078	H-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 parameters	Δρmax = 0.28 e Å−3
0 restraints	Δρmin = −0.25 e Å−3

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.

	x	y	z	Uiso*/Ueq
S5	0.108822 (18)	0.10694 (4)	0.60102 (3)	0.02112 (11)
S5A	0.45872 (2)	0.62119 (4)	0.66155 (3)	0.03086 (12)
N3A	0.31415 (6)	0.88825 (12)	0.75775 (9)	0.0224 (3)
N3	0.19707 (6)	0.41535 (12)	0.44021 (8)	0.0206 (3)
C2A	0.33340 (8)	0.87296 (15)	0.85980 (11)	0.0248 (3)
H2A	0.3066	0.9241	0.9062	0.030*
C2	0.19194 (7)	0.34543 (15)	0.34913 (10)	0.0223 (3)
H2	0.2092	0.3942	0.2917	0.027*
N1A	0.38455 (6)	0.79651 (13)	0.90461 (9)	0.0271 (3)
N1	0.16633 (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)
N4	0.18145 (6)	0.41308 (12)	0.61780 (8)	0.0198 (3)
H4	0.1750	0.3622	0.6737	0.024*
N4A	0.33088 (6)	0.82477 (13)	0.58732 (9)	0.0238 (3)
H4A	0.3504	0.7673	0.5443	0.029*
C4	0.17530 (6)	0.34889 (14)	0.52409 (10)	0.0170 (3)
C4A	0.34922 (7)	0.81394 (14)	0.68957 (10)	0.0193 (3)
C7A	0.47914 (8)	0.63230 (16)	0.86262 (13)	0.0323 (4)
H7A	0.4982	0.6165	0.9321	0.039*
C7	0.10891 (7)	0.01643 (15)	0.41142 (10)	0.0221 (3)
H7	0.1017	−0.0415	0.3511	0.026*
C6A	0.50344 (8)	0.57307 (18)	0.77755 (13)	0.0373 (4)
H6A	0.5419	0.5103	0.7809	0.045*
C6	0.08920 (7)	−0.01926 (15)	0.50635 (11)	0.0232 (3)
H6	0.0666	−0.1058	0.5199	0.028*
C9	0.19815 (7)	0.56162 (15)	0.63204 (11)	0.0232 (3)
H9A	0.2132	0.6007	0.5658	0.028*
H9B	0.2371	0.5716	0.6862	0.028*
C9A	0.28012 (7)	0.92695 (16)	0.54290 (11)	0.0275 (3)
H9D	0.2434	0.9403	0.5917	0.033*
H9C	0.2581	0.8894	0.4764	0.033*
C10A	0.31332 (7)	1.06765 (16)	0.52284 (11)	0.0264 (3)
C10	0.13638 (7)	0.64490 (14)	0.66460 (10)	0.0194 (3)
C11	0.06933 (7)	0.60827 (14)	0.62788 (11)	0.0227 (3)
H11	0.0622	0.5333	0.5790	0.027*
C11A	0.32231 (7)	1.16842 (17)	0.60148 (12)	0.0297 (3)
H11A	0.3050	1.1508	0.6676	0.036*
C12A	0.35621 (8)	1.29412 (17)	0.58469 (13)	0.0344 (4)
H12A	0.3618	1.3624	0.6390	0.041*
C12	0.01270 (8)	0.68002 (15)	0.66191 (12)	0.0285 (3)
H12	−0.0329	0.6538	0.6364	0.034*
C13	0.02237 (8)	0.78964 (15)	0.73294 (12)	0.0291 (3)
H13	−0.0164	0.8380	0.7570	0.035*
C13A	0.38197 (8)	1.32031 (18)	0.48879 (13)	0.0360 (4)
H13A	0.4061	1.4057	0.4776	0.043*
C14	0.08889 (8)	0.82823 (15)	0.76859 (11)	0.0265 (3)
H14	0.0959	0.9042	0.8167	0.032*
C14A	0.37252 (9)	1.22257 (19)	0.40976 (13)	0.0388 (4)
H14A	0.3895	1.2412	0.3435	0.047*
C15A	0.33837 (8)	1.09711 (18)	0.42644 (12)	0.0328 (4)
H15A	0.3320	1.0302	0.3713	0.039*
C15	0.14548 (7)	0.75657 (14)	0.73447 (11)	0.0228 (3)
H15	0.1910	0.7842	0.7592	0.027*

	U11	U22	U33	U12	U13	U23
S5	0.0280 (2)	0.01963 (19)	0.01620 (18)	−0.00222 (13)	0.00445 (14)	0.00056 (13)
S5A	0.0272 (2)	0.0318 (2)	0.0339 (2)	0.00627 (15)	0.00492 (16)	−0.00622 (16)
N3A	0.0211 (6)	0.0247 (6)	0.0218 (6)	0.0000 (5)	0.0039 (5)	−0.0010 (5)
N3	0.0206 (6)	0.0243 (6)	0.0169 (6)	−0.0002 (5)	0.0024 (5)	0.0031 (5)
C2A	0.0263 (8)	0.0272 (8)	0.0217 (7)	−0.0011 (6)	0.0061 (6)	−0.0019 (6)
C2	0.0221 (7)	0.0294 (8)	0.0158 (7)	0.0000 (6)	0.0033 (5)	0.0041 (6)
N1A	0.0291 (7)	0.0310 (7)	0.0212 (6)	−0.0007 (5)	0.0017 (5)	0.0004 (5)
N1	0.0233 (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)
N4	0.0260 (6)	0.0182 (6)	0.0155 (6)	−0.0013 (5)	0.0037 (5)	0.0004 (5)
N4A	0.0262 (6)	0.0262 (7)	0.0191 (6)	0.0014 (5)	0.0020 (5)	−0.0008 (5)
C4	0.0137 (6)	0.0205 (7)	0.0168 (7)	0.0047 (5)	0.0010 (5)	0.0014 (5)
C4A	0.0176 (7)	0.0198 (7)	0.0206 (7)	−0.0062 (5)	0.0029 (5)	0.0000 (6)
C7A	0.0294 (8)	0.0327 (9)	0.0334 (9)	0.0006 (7)	−0.0069 (7)	0.0046 (7)
C7	0.0253 (7)	0.0220 (7)	0.0186 (7)	0.0034 (6)	−0.0009 (6)	−0.0042 (6)
C6A	0.0272 (9)	0.0331 (9)	0.0505 (11)	0.0095 (7)	−0.0028 (7)	0.0015 (8)
C6	0.0257 (8)	0.0191 (7)	0.0247 (7)	−0.0002 (6)	0.0003 (6)	−0.0014 (6)
C9	0.0240 (8)	0.0222 (7)	0.0239 (7)	−0.0042 (6)	0.0050 (6)	−0.0033 (6)
C9A	0.0221 (8)	0.0361 (9)	0.0237 (7)	0.0012 (6)	−0.0027 (6)	0.0028 (6)
C10A	0.0176 (7)	0.0332 (8)	0.0280 (8)	0.0066 (6)	−0.0013 (6)	0.0080 (7)
C10	0.0238 (7)	0.0174 (7)	0.0173 (7)	−0.0019 (5)	0.0033 (5)	0.0040 (5)
C11	0.0281 (8)	0.0181 (7)	0.0213 (7)	−0.0005 (6)	−0.0015 (6)	0.0008 (6)
C11A	0.0234 (8)	0.0353 (9)	0.0307 (8)	0.0056 (6)	0.0036 (6)	0.0045 (7)
C12A	0.0296 (9)	0.0320 (9)	0.0413 (10)	0.0048 (7)	0.0009 (7)	0.0031 (7)
C12	0.0239 (8)	0.0245 (8)	0.0367 (9)	0.0009 (6)	−0.0007 (6)	0.0057 (7)
C13	0.0315 (9)	0.0209 (8)	0.0360 (8)	0.0064 (6)	0.0105 (7)	0.0058 (6)
C13A	0.0299 (9)	0.0316 (9)	0.0465 (10)	0.0038 (7)	0.0026 (7)	0.0133 (8)
C14	0.0398 (9)	0.0161 (7)	0.0245 (8)	−0.0010 (6)	0.0078 (6)	−0.0002 (6)
C14A	0.0365 (9)	0.0459 (10)	0.0344 (9)	0.0039 (8)	0.0050 (7)	0.0172 (8)
C15A	0.0330 (9)	0.0384 (9)	0.0266 (8)	0.0055 (7)	0.0000 (7)	0.0067 (7)
C15	0.0275 (8)	0.0190 (7)	0.0218 (7)	−0.0055 (6)	0.0025 (6)	0.0016 (6)

S5—C6	1.7246 (14)	C6A—H6A	0.9500
S5—C4'	1.7277 (13)	C6—H6	0.9500
S5A—C6A	1.7245 (17)	C9—C10	1.5159 (19)
S5A—C4A'	1.7266 (14)	C9—H9A	0.9900
N3A—C2A	1.3410 (19)	C9—H9B	0.9900
N3A—C4A	1.3447 (18)	C9A—C10A	1.509 (2)
N3—C2	1.3395 (18)	C9A—H9D	0.9900
N3—C4	1.3408 (17)	C9A—H9C	0.9900
C2A—N1A	1.3216 (19)	C10A—C11A	1.389 (2)
C2A—H2A	0.9500	C10A—C15A	1.389 (2)
C2—N1	1.3228 (19)	C10—C15	1.3880 (19)
C2—H2	0.9500	C10—C11	1.390 (2)
N1A—C7A'	1.3671 (19)	C11—C12	1.387 (2)
N1—C7'	1.3660 (17)	C11—H11	0.9500
C7A'—C4A'	1.387 (2)	C11A—C12A	1.383 (2)
C7A'—C7A	1.427 (2)	C11A—H11A	0.9500
C7'—C4'	1.3918 (18)	C12A—C13A	1.383 (2)
C7'—C7	1.428 (2)	C12A—H12A	0.9500
C4A'—C4A	1.4127 (19)	C12—C13	1.384 (2)
C4'—C4	1.4112 (19)	C12—H12	0.9500
N4—C4	1.3436 (17)	C13—C14	1.382 (2)
N4—C9	1.4507 (18)	C13—H13	0.9500
N4—H4	0.8800	C13A—C14A	1.374 (2)
N4A—C4A	1.3361 (17)	C13A—H13A	0.9500
N4A—C9A	1.4626 (18)	C14—C15	1.386 (2)
N4A—H4A	0.8800	C14—H14	0.9500
C7A—C6A	1.342 (2)	C14A—C15A	1.383 (2)
C7A—H7A	0.9500	C14A—H14A	0.9500
C7—C6	1.3457 (19)	C15A—H15A	0.9500
C7—H7	0.9500	C15—H15	0.9500
C6—S5—C4'	90.65 (6)	N4—C9—C10	111.45 (11)
C6A—S5A—C4A'	90.33 (7)	N4—C9—H9A	109.3
C2A—N3A—C4A	117.47 (12)	C10—C9—H9A	109.3
C2—N3—C4	117.42 (12)	N4—C9—H9B	109.3
N1A—C2A—N3A	128.83 (13)	C10—C9—H9B	109.3
N1A—C2A—H2A	115.6	H9A—C9—H9B	108.0
N3A—C2A—H2A	115.6	N4A—C9A—C10A	111.58 (11)
N1—C2—N3	129.24 (13)	N4A—C9A—H9D	109.3
N1—C2—H2	115.4	C10A—C9A—H9D	109.3
N3—C2—H2	115.4	N4A—C9A—H9C	109.3
C2A—N1A—C7A'	114.19 (12)	C10A—C9A—H9C	109.3
C2—N1—C7'	113.79 (11)	H9D—C9A—H9C	108.0
N1A—C7A'—C4A'	121.81 (13)	C11A—C10A—C15A	118.36 (15)
N1A—C7A'—C7A	126.04 (13)	C11A—C10A—C9A	120.90 (13)
C4A'—C7A'—C7A	112.15 (13)	C15A—C10A—C9A	120.68 (14)
N1—C7'—C4'	121.84 (13)	C15—C10—C11	118.57 (13)
N1—C7'—C7	126.25 (12)	C15—C10—C9	120.62 (12)
C4'—C7'—C7	111.89 (12)	C11—C10—C9	120.78 (12)
C7A'—C4A'—C4A	119.06 (12)	C12—C11—C10	120.68 (13)
C7A'—C4A'—S5A	111.77 (11)	C12—C11—H11	119.7
C4A—C4A'—S5A	129.15 (11)	C10—C11—H11	119.7
C7'—C4'—C4	119.06 (12)	C12A—C11A—C10A	120.81 (14)
C7'—C4'—S5	111.67 (10)	C12A—C11A—H11A	119.6
C4—C4'—S5	129.22 (10)	C10A—C11A—H11A	119.6
C4—N4—C9	123.67 (11)	C11A—C12A—C13A	119.95 (16)
C4—N4—H4	118.2	C11A—C12A—H12A	120.0
C9—N4—H4	118.2	C13A—C12A—H12A	120.0
C4A—N4A—C9A	123.62 (12)	C13—C12—C11	120.22 (14)
C4A—N4A—H4A	118.2	C13—C12—H12	119.9
C9A—N4A—H4A	118.2	C11—C12—H12	119.9
N3—C4—N4	119.55 (12)	C14—C13—C12	119.49 (14)
N3—C4—C4'	118.59 (12)	C14—C13—H13	120.3
N4—C4—C4'	121.85 (12)	C12—C13—H13	120.3
N4A—C4A—N3A	119.21 (12)	C14A—C13A—C12A	119.88 (16)
N4A—C4A—C4A'	122.19 (12)	C14A—C13A—H13A	120.1
N3A—C4A—C4A'	118.60 (12)	C12A—C13A—H13A	120.1
C6A—C7A—C7A'	111.74 (14)	C13—C14—C15	120.26 (14)
C6A—C7A—H7A	124.1	C13—C14—H14	119.9
C7A'—C7A—H7A	124.1	C15—C14—H14	119.9
C6—C7—C7'	112.17 (12)	C13A—C14A—C15A	120.15 (16)
C6—C7—H7	123.9	C13A—C14A—H14A	119.9
C7'—C7—H7	123.9	C15A—C14A—H14A	119.9
C7A—C6A—S5A	114.02 (12)	C14A—C15A—C10A	120.83 (16)
C7A—C6A—H6A	123.0	C14A—C15A—H15A	119.6
S5A—C6A—H6A	123.0	C10A—C15A—H15A	119.6
C7—C6—S5	113.61 (11)	C14—C15—C10	120.76 (13)
C7—C6—H6	123.2	C14—C15—H15	119.6
S5—C6—H6	123.2	C10—C15—H15	119.6

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4···N1i	0.88	2.13	2.999 (2)	167
N4A—H4A···N1Aii	0.88	2.05	2.872 (2)	156
C7—H7···Cgiii	0.95	2.58	3.5317 (13)	175
C2A—H2A···N3iv	0.95	2.67	3.527 (2)	150
C15—H15···N3A	0.95	2.58	3.4842 (18)	159

Table 1

Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C10–C15 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4⋯N1i	0.88	2.13	2.999 (2)	167
N4A—H4A⋯N1A ii	0.88	2.05	2.872 (2)	156
C7—H7⋯Cg iii	0.95	2.58	3.5317 (13)	175
C2A—H2A⋯N3iv	0.95	2.67	3.527 (2)	150
C15—H15⋯N3A	0.95	2.58	3.4842 (18)	159

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .