4-Amino-6-(2,2-diethoxy­ethoxy)-2-(methyl­sulfan­yl)pyrimidine

Quijano, M.L.; Cobo, J.; Nogueras, M.; Low, J.N.

doi:10.1107/S1600536806024536

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 62| Part 8| August 2006| Pages o3142-o3144

https://doi.org/10.1107/S1600536806024536

4-Amino-6-(2,2-diethoxyethoxy)-2-(methylsulfanyl)pyrimidine

Maria Luisa Quijano,^a Justo Cobo,^a Manuel Nogueras ^a and John Nicolson Low ^b ^*

^aDepartamento de Química Inorgánica y Orgánica, Universidad de Jaén, 23071 Jaén, Spain, and ^bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland.
^*Correspondence e-mail: che562@abdn.ac.uk

(Received 21 June 2006; accepted 26 June 2006; online 6 July 2006)

The supramolecular structure of the title compound, C₁₁H₁₉N₃O₃S, consists of a ribbon of alternating centrosymmetric R₂²(8) and R₂²(18) rings.

Comment

The title compound, (I), was prepared as an intermediate for the preparation of fused pyrimidine systems in our ongoing programme aimed at the development of novel syntheses of fused heterocyclic systems. The bond lengths and angles show no unusual features.

Atom N4 in the molecule at (x, y, z) acts via H4A as a hydrogen-bond donor to atom N3 in the molecule at (1 − x, 1 − y, −z), so generating by inversion an R₂²(8) (Bernstein et al., 1995 ) ring centred at (½, ½, 0). Atom N4 at (x, y, z) acts as a hydrogen-bond donor via atom H4B to atom O62 in the molecule at (−x, 1 − y, 1 − z), so generating by inversion an R₂²(18) ring centred at (0, ½, ½). Propagation by inversion of these two hydrogen bonds then generates a chain of alternating R₂²(8) and R₂²(18) rings running parallel to the [ $[\overline{1}]$ 01] direction with the R₂²(8) rings centred at (½ − n, ½, n) (n = zero or an integer) and the R₂²(18) rings centred at (n, ½, ½ − n) (n = zero or an integer). There are no direction-specific interactions between adjacent chains.

Figure 1
A view of the molecular structure of (I)

with the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms as spheres of arbitrary radii.

Figure 2
A stereoscopic view of the ribbon formed by alternating R₂²(8) and R₂²(18) centrosymmetric dimers. H atoms bonded to C atoms have been omitted.

Experimental

To a solution of 4-amino-2-(methylsulfanyl)pyrimidin-6(1H)-one (20 mmol) in dry dimethylformamide (40 ml) was added solid anhydrous sodium carbonate (30 mmol). The mixture was stirred at room temperature for 10 min, bromoacetaldehyde diethyl acetal (60 mmol) was added and the final mixture heated at 363 K for 15 h. Water (20 ml) was added and the mixture was then poured on to crushed ice. The resultant solid was collected by filtration and washed with cold water to give the title compound in 85% yield. This solid was recrystallized from methanol to give light-yellow crystalline micaceous blocks. HRMS found 273.1161, calculated for C₁₁H₁₉N₃O₃S 273.1147.

Crystal data

C₁₁H₁₉N₃O₃S
M_r = 273.35
Triclinic, $[P \overline 1]$
a = 7.2278 (8) Å
b = 9.6358 (9) Å
c = 10.0852 (10) Å
α = 81.197 (9)°
β = 82.390 (7)°
γ = 78.818 (8)°
V = 677.12 (12) Å³
Z = 2
D_x = 1.341 Mg m⁻³
Mo Kα radiation
μ = 0.24 mm⁻¹
T = 120 (2) K
Block, yellow
0.52 × 0.29 × 0.14 mm

Data collection

Bruker–Nonius KappaCCD diffractometer
Thick–slice φ and ω scans
Absorption correction: multi-scan (EVALCCD; Duisenberg et al., 2003 ) T_min = 0.884, T_max = 0.967
10168 measured reflections
3000 independent reflections
1200 reflections with I > 2σ(I)
R_int = 0.118
θ_max = 27.5°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.073
wR(F²) = 0.253
S = 1.02
3000 reflections
166 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.1062P)² + 1.0232P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.70 e Å⁻³
Δρ_min = −0.53 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4A⋯N3ⁱ	1.00	2.07	3.052 (6)	167
N4—H4B⋯O62ⁱⁱ	0.91	2.05	2.919 (6)	158
Symmetry codes: (i) -x+1, -y+1, -z; (ii) -x, -y+1, -z+1.

H atoms were treated as riding atoms, with aromatic C—H = 0.95 Å, aliphatic C—H = 1.00 Å and CH₂ C—H = 0.99 Å, with U_iso(H) = 1.2U_eq(C), methyl C—H = 0.98 Å, with U_iso(H) = 1.5U_eq(C), and N—H = 0.92 and 1.00 Å, with U_iso = 1.2U_eq(N). In the case of atom N4, atoms H4A and H4B were located in a difference map, refined and then treated as riding atoms in the latter stages of refinement. The difference map showed that the peak related to H4A was extended from N4 lying along the N4⋯N3ⁱ [symmetry code: (i) 1 − x, 1 − y, −z] vector. The methyl H atoms of the methylsulfanyl group were modelled as six equally spaced half-H atoms. The crystal quality was generally poor due to the micaceous habit of the crystals; this has resulted in a high R_int value and a low ratio of observed/unique reflections.

Data collection: COLLECT (Bruker–Nonius, 2004 ); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000 ); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005 ); program(s) used to refine structure: OSCAIL (McArdle, 2003 ) and SHELXL97 (Sheldrick, 1997 ); molecular graphics: ORTEPII (Johnson, 1976 ) and PLATON (Spek, 2003 ); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536806024536/lh2112sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806024536/lh2112Isup2.hkl

Computing details top

Data collection: COLLECT (Bruker–Nonius, 2004); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

4-amino-6-(2,2-diethoxyethoxy)-2-(methylsulfanyl)pyrimidine top

Crystal data top

C₁₁H₁₉N₃O₃S	Z = 2
M_r = 273.35	F(000) = 292
Triclinic, P1	D_x = 1.341 Mg m⁻³
Hall symbol: -P 1	Melting point: 438 K
a = 7.2280 (8) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.6360 (9) Å	Cell parameters from 3000 reflections
c = 10.085 (1) Å	θ = 5.1–27.5°
α = 81.197 (9)°	µ = 0.24 mm⁻¹
β = 82.390 (7)°	T = 120 K
γ = 78.817 (8)°	Block, yellow
V = 677.12 (12) Å³	0.52 × 0.29 × 0.14 mm

Data collection top

Bruker–Nonius KappaCCD diffractometer	1200 reflections with I > 2σ(I)
Thick–slice π and ω scans	R_int = 0.118
Absorption correction: multi-scan (EvalCCD; Duisenberg et al., 2003)	θ_max = 27.5°, θ_min = 5.1°
T_min = 0.884, T_max = 0.967	h = −8→9
10168 measured reflections	k = −12→12
3000 independent reflections	l = −13→12

Refinement top

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)] = 0.073	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.253	H-atom parameters constrained
S = 1.02	w = 1/[σ²(F_o²) + (0.1062P)² + 1.0232P] where P = (F_o² + 2F_c²)/3
3000 reflections	(Δ/σ)_max < 0.001
166 parameters	Δρ_max = 0.70 e Å⁻³
0 restraints	Δρ_min = −0.53 e Å⁻³

Special details top

Experimental. The scale factors in the experimental table are calculated from the 'size' command in the SHELXL97 input file.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
N1	0.4599 (6)	0.6665 (4)	0.3719 (4)	0.0270 (10)
C2	0.5473 (7)	0.6411 (5)	0.2507 (5)	0.0281 (12)
S2	0.7579 (2)	0.70417 (16)	0.19170 (14)	0.0373 (5)
C21	0.7992 (8)	0.7871 (6)	0.3302 (6)	0.0401 (15)
N3	0.4967 (6)	0.5670 (4)	0.1636 (4)	0.0246 (10)
C4	0.3395 (7)	0.5080 (5)	0.2048 (5)	0.0266 (12)
N4	0.2892 (6)	0.4329 (5)	0.1184 (4)	0.0317 (11)
C5	0.2369 (7)	0.5264 (5)	0.3319 (5)	0.0278 (12)
C6	0.3043 (7)	0.6092 (5)	0.4078 (5)	0.0252 (12)
O6	0.2063 (5)	0.6314 (4)	0.5289 (3)	0.0318 (9)
C61	0.2784 (8)	0.7194 (6)	0.6052 (5)	0.0317 (13)
C62	0.1616 (7)	0.7193 (6)	0.7414 (5)	0.0307 (13)
O61	0.2315 (5)	0.8144 (4)	0.8062 (3)	0.0325 (9)
C63	0.1706 (9)	0.8063 (6)	0.9472 (5)	0.0377 (14)
C64	0.2834 (9)	0.8905 (6)	1.0088 (6)	0.0455 (16)
O62	−0.0357 (5)	0.7540 (4)	0.7356 (3)	0.0307 (9)
C65	−0.1042 (8)	0.8906 (6)	0.6607 (5)	0.0359 (14)
C66	−0.3171 (8)	0.9162 (6)	0.6835 (6)	0.0428 (15)
H21A	0.9162	0.8266	0.3072	0.060*	0.50
H21B	0.8115	0.7160	0.4106	0.060*	0.50
H21C	0.6924	0.8640	0.3484	0.060*	0.50
H21D	0.6972	0.7778	0.4036	0.060*	0.50
H21E	0.8019	0.8884	0.3002	0.060*	0.50
H21F	0.9210	0.7404	0.3624	0.060*	0.50
H4A	0.3713	0.4190	0.0323	0.038*
H4B	0.1858	0.3925	0.1537	0.038*
H5	0.1280	0.4843	0.3632	0.033*
H61A	0.2684	0.8179	0.5574	0.038*
H61B	0.4135	0.6812	0.6168	0.038*
H62	0.1910	0.6218	0.7929	0.037*
H63A	0.1914	0.7056	0.9896	0.045*
H63B	0.0337	0.8460	0.9619	0.045*
H64A	0.2631	0.9896	0.9654	0.068*
H64B	0.4184	0.8491	0.9955	0.068*
H64C	0.2421	0.8878	1.1056	0.068*
H65A	−0.0615	0.8898	0.5633	0.043*
H65B	−0.0547	0.9672	0.6925	0.043*
H66A	−0.3576	0.9137	0.7804	0.064*
H66B	−0.3647	0.8419	0.6486	0.064*
H66C	−0.3680	1.0098	0.6365	0.064*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.030 (3)	0.031 (2)	0.021 (2)	−0.011 (2)	−0.0009 (19)	−0.0021 (18)
C2	0.026 (3)	0.033 (3)	0.026 (3)	−0.006 (2)	−0.005 (2)	−0.003 (2)
S2	0.0361 (9)	0.0440 (9)	0.0357 (8)	−0.0165 (7)	0.0007 (6)	−0.0091 (6)
C21	0.034 (4)	0.041 (3)	0.051 (3)	−0.016 (3)	−0.002 (3)	−0.017 (3)
N3	0.025 (3)	0.028 (2)	0.022 (2)	−0.007 (2)	−0.0029 (18)	−0.0031 (18)
C4	0.026 (3)	0.027 (3)	0.027 (3)	−0.003 (2)	−0.004 (2)	−0.005 (2)
N4	0.029 (3)	0.047 (3)	0.025 (2)	−0.019 (2)	0.0042 (19)	−0.014 (2)
C5	0.026 (3)	0.028 (3)	0.029 (3)	−0.005 (2)	0.000 (2)	−0.007 (2)
C6	0.021 (3)	0.027 (3)	0.025 (3)	−0.001 (2)	−0.002 (2)	−0.002 (2)
O6	0.030 (2)	0.042 (2)	0.0268 (18)	−0.0138 (18)	0.0040 (16)	−0.0128 (16)
C61	0.032 (3)	0.038 (3)	0.028 (3)	−0.006 (3)	−0.003 (2)	−0.012 (2)
C62	0.027 (3)	0.035 (3)	0.033 (3)	−0.008 (3)	−0.004 (2)	−0.005 (2)
O61	0.032 (2)	0.044 (2)	0.0250 (17)	−0.0116 (18)	−0.0007 (15)	−0.0112 (16)
C63	0.045 (4)	0.043 (3)	0.024 (3)	−0.008 (3)	0.002 (2)	−0.005 (2)
C64	0.057 (4)	0.046 (4)	0.036 (3)	−0.006 (3)	−0.013 (3)	−0.010 (3)
O62	0.027 (2)	0.030 (2)	0.0335 (19)	−0.0045 (17)	−0.0013 (16)	−0.0045 (16)
C65	0.036 (4)	0.037 (3)	0.037 (3)	−0.011 (3)	−0.005 (3)	−0.004 (3)
C66	0.028 (3)	0.048 (4)	0.048 (3)	−0.001 (3)	−0.003 (3)	−0.003 (3)

Geometric parameters (Å, º) top

N1—C6	1.331 (6)	C61—C62	1.514 (7)
N1—C2	1.335 (6)	C61—H61A	0.99
C2—N3	1.339 (6)	C61—H61B	0.99
C2—S2	1.746 (5)	C62—O61	1.404 (6)
S2—C21	1.796 (5)	C62—O62	1.407 (6)
C21—H21A	0.98	C62—H62	1.00
C21—H21B	0.98	O61—C63	1.427 (6)
C21—H21C	0.98	C63—C64	1.501 (7)
C21—H21D	0.98	C63—H63A	0.99
C21—H21E	0.98	C63—H63B	0.99
C21—H21F	0.98	C64—H64A	0.98
N3—C4	1.357 (6)	C64—H64B	0.98
C4—N4	1.340 (6)	C64—H64C	0.98
C4—C5	1.411 (7)	O62—C65	1.446 (6)
N4—H4A	0.9959	C65—C66	1.503 (8)
N4—H4B	0.9151	C65—H65A	0.99
C5—C6	1.377 (7)	C65—H65B	0.99
C5—H5	0.95	C66—H66A	0.98
C6—O6	1.354 (6)	C66—H66B	0.98
O6—C61	1.435 (6)	C66—H66C	0.98

C6—N1—C2	114.3 (4)	C6—O6—C61	116.0 (4)
N1—C2—N3	128.0 (5)	O6—C61—C62	107.8 (4)
N1—C2—S2	119.7 (4)	O6—C61—H61A	110.1
N3—C2—S2	112.3 (4)	C62—C61—H61A	110.1
C2—S2—C21	102.8 (3)	O6—C61—H61B	110.1
S2—C21—H21A	109.5	C62—C61—H61B	110.1
S2—C21—H21B	109.5	H61A—C61—H61B	108.5
H21A—C21—H21B	109.5	O61—C62—O62	113.1 (4)
S2—C21—H21C	109.5	O61—C62—C61	104.5 (4)
H21A—C21—H21C	109.5	O62—C62—C61	114.6 (4)
H21B—C21—H21C	109.5	O61—C62—H62	108.1
S2—C21—H21D	109.5	O62—C62—H62	108.1
H21A—C21—H21D	141.1	C61—C62—H62	108.1
H21B—C21—H21D	56.3	C62—O61—C63	113.5 (4)
H21C—C21—H21D	56.3	O61—C63—C64	108.1 (5)
S2—C21—H21E	109.5	O61—C63—H63A	110.1
H21A—C21—H21E	56.3	C64—C63—H63A	110.1
H21B—C21—H21E	141.1	O61—C63—H63B	110.1
H21C—C21—H21E	56.3	C64—C63—H63B	110.1
H21D—C21—H21E	109.5	H63A—C63—H63B	108.4
S2—C21—H21F	109.5	C63—C64—H64A	109.5
H21A—C21—H21F	56.3	C63—C64—H64B	109.5
H21B—C21—H21F	56.3	H64A—C64—H64B	109.5
H21C—C21—H21F	141.1	C63—C64—H64C	109.5
H21D—C21—H21F	109.5	H64A—C64—H64C	109.5
H21E—C21—H21F	109.5	H64B—C64—H64C	109.5
C2—N3—C4	116.0 (4)	C62—O62—C65	115.9 (4)
N4—C4—N3	116.2 (4)	O62—C65—C66	107.5 (4)
N4—C4—C5	122.9 (5)	O62—C65—H65A	110.2
N3—C4—C5	120.9 (4)	C66—C65—H65A	110.2
C4—N4—H4A	119.3	O62—C65—H65B	110.2
C4—N4—H4B	111.8	C66—C65—H65B	110.2
H4A—N4—H4B	128.5	H65A—C65—H65B	108.5
C6—C5—C4	115.9 (5)	C65—C66—H66A	109.5
C6—C5—H5	122.1	C65—C66—H66B	109.5
C4—C5—H5	122.1	H66A—C66—H66B	109.5
N1—C6—O6	117.9 (4)	C65—C66—H66C	109.5
N1—C6—C5	124.9 (4)	H66A—C66—H66C	109.5
O6—C6—C5	117.2 (4)	H66B—C66—H66C	109.5

C6—N1—C2—N3	0.3 (7)	C4—C5—C6—O6	178.6 (4)
C6—N1—C2—S2	−177.9 (3)	N1—C6—O6—C61	1.9 (6)
N1—C2—S2—C21	2.1 (5)	C5—C6—O6—C61	−179.3 (4)
N3—C2—S2—C21	−176.3 (4)	C6—O6—C61—C62	−174.7 (4)
N1—C2—N3—C4	−1.5 (7)	O6—C61—C62—O61	−176.2 (4)
S2—C2—N3—C4	176.8 (3)	O6—C61—C62—O62	−51.8 (6)
C2—N3—C4—N4	−179.6 (4)	O62—C62—O61—C63	68.0 (5)
C2—N3—C4—C5	0.6 (7)	C61—C62—O61—C63	−166.7 (4)
N4—C4—C5—C6	−178.5 (5)	C62—O61—C63—C64	169.2 (4)
N3—C4—C5—C6	1.3 (7)	O61—C62—O62—C65	62.1 (5)
C2—N1—C6—O6	−179.3 (4)	C61—C62—O62—C65	−57.5 (6)
C2—N1—C6—C5	2.0 (7)	C62—O62—C65—C66	−171.9 (4)
C4—C5—C6—N1	−2.7 (7)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4A···N3ⁱ	1.00	2.07	3.052 (6)	167
N4—H4B···O62ⁱⁱ	0.91	2.05	2.919 (6)	158

Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x, −y+1, −z+1.

Acknowledgements

MLQ, MN and JC thank the Consejería de Innovación, Ciencia y Empresa (Junta de Andalucía, Spain) and the Universidad de Jaén for financial support.

References

Bernstein, J., Davis, R., Shimoni, L. & Chang, N.-L. (1995). Agnew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Google Scholar
Bruker–Nonius (2004). COLLECT. Bruker–Nonius BV, Delft, The Netherlands. Google Scholar
Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381–388. Web of Science CrossRef CAS IUCr Journals Google Scholar
Duisenberg, A. J. M., Hooft, R. W. W., Schreurs, A. M. M. & Kroon, J. (2000). J. Appl. Cryst. 33, 893–898. Web of Science CrossRef CAS IUCr Journals Google Scholar
Duisenberg, A. J. M., Kroon-Batenburg, L. M. J. & Schreurs, A. M. M. (2003). J. Appl. Cryst. 36, 220–229. Web of Science CrossRef CAS IUCr Journals Google Scholar
Ferguson, G. (1999). PRPKAPPA. University of Guelph, Canada. Google Scholar
Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. Google Scholar
McArdle, P. (2003). OSCAIL for Windows. Version 10. Crystallography Centre, Chemistry Department, NUI Galway, Ireland. Google Scholar
Sheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany. Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar

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