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In the title compound, C14H15N5O2, the intramolecular dimensions are consistent with a highly polarized electronic structure. The mol­ecules are linked into chains by a combination of N—H...N, N—H...O and N—H...π(arene) hydrogen bonds, and the chains are linked in pairs by aromatic π–π-stacking interactions

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270102010387/na1579sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270102010387/na1579Isup2.hkl
Contains datablock I

CCDC reference: 192996

Comment top

Alkoxy- and amino-substituted O6-benzyloxy-5-nitrosopyrimidines (Marchal et al., 2000, 2002) are important as potential, or proven, in vitro inhibitors of the human DNA repair protein O6-alkylguanine-DNA-transferase (Chae et al., 1995; Quesada, Marchal et al., 2002). We report here the molecular and supramolecular structure of an analogue, 4-(allylamino)-2-amino-6-benzyloxy-5-nitrosopyrimidine, (I), containing an N-allyl substituent.

The intramolecular dimensions of (I) (Table 1) show a number of features typical of substituted 5-nitrosopyrimidines (Low et al., 2000; Quesada, Marchal et al., 2002); in particular, the sequence of four C—N bonds between N2 and N4 (Fig. 1) spans only a very small range of distances, 1.329 (2)–1.339 (2) Å, while the bond C6—N1 is significantly shorter and C2—N1 is significantly longer; the distances C4—C5 and C5—C6 are rather similar; and, in addition, the C—N and N—O distances in each C-nitroso fragment differ by only ca 0.11 Å, whereas in simple neutral compounds, where there is no possibility of significant electronic delocalization, these distances normally differ by at least 0.20 Å (Talberg, 1977; Schlemper et al., 1986) and the NO distance rarely exceeds 1.25 Å (Davis et al., 1965; Bauer & Andreassen, 1972; Talberg, 1977; Schlemper et al., 1986). These observations all point to the charge-separated form (Ia) as an important contributor to the overall electronic structure, at the expense of classically bond-fixed forms, such as (Ib) and (Ic).

The nitrosyl O atom is almost coplanar with the pyrimidine ring (Table 2). This is associated both with the electronic delocalization and with the intramolecular hydrogen bond (see below). Similarly, the torsion angles indicate that atom C7 of the allylamino substituent, and both C67 and C61 of the benzyloxy substituent, are also nearly coplanar with the pyrimidine ring; however, there are substantial twists away from planarity around the N4—C7 and C61—C67 bonds.

There is an intramolecular N—H···O hydrogen bond (Table 2) generating an S(6) motif (Bernstein et al., 1995); the N—H···O angle is small, constrained both by the ring size and shape and by the near coplanarity of the nitroso group and the pyrimidine ring, but both donor and acceptor in this interaction carry partial charges [cf. structure (Ia)], and hence this interaction is an example of a resonance-assisted hydrogen bond (Gilli et al., 1994). The molecules are linked by further hydrogen bonds into chains running parallel to the [001] direction. Amino atom N2 acts as hydrogen-bond donor, via H2A, to both N5i and O6i [symmetry code: (i) x, y, 1 + z], so generating by translation a C(6) C(7)[R21(5)] chain of rings (Fig. 2). This three-centre N—H···(N,O) hydrogen bond has a sum of the angles at H2A of 355°, but the H···O distance is long and the N—H···O angle is small (Table 2); hence, it may be that the H···O contact is more adventitious than significant. The conventional chain-forming hydrogen bonds are augmented by an N—H···π(arene) interaction; amino atom N2 also acts as donor, via H2B, which is not involved in any conventional hydrogen bonds, to the centroid (Cg2i) of arene ring C61–C66 (Table 2 and Fig. 2).

Four [001] chains run through each unit cell, two in the domain 0.29 < y < 0.71 and two in the domain 0.79 < y < 1.21. Within each domain, the [001] chains are pairwise linked by ππ-stacking interactions; the parallel pyrimidine rings in the molecules at (x, y, z) and (-x, 1 - y, 1 - z) have an interplanar spacing of 3.310 (2) Å and a centroid separation of 3.779 (2) Å (Fig. 3). While the ring-centroid offset, ca 1.82 Å, is quite large, the offset direction is such that cationic and anionic regions of the adjacent molecules [cf. structure (Ia)] are reasonably close (Fig. 3), thus enhancing this attractive interaction.

All three independent N—H bonds in (I) are thus involved in the overall hydrogen bonding, with each forming a different type of interaction. Although the hard (Braga et al., 1995) hydrogen-bond donors are all utilized, unusually (Low et al., 2000; Quesada, Marchal et al. 2002) there are neither hard intermolecular hydrogen bonds involving the nitrosyl atom O5 nor any soft hydrogen bonds involving atom O5.

Experimental top

A sample of (I) was prepared by reaction of 2-amino-4,6-bis(benzyloxy)-5-nitrosopyrimidine (Quesada, Low et al., 2002) with allylamine in ethanol at ambient temperature. Crystals suitable for single-crystal X-ray diffraction analysis were grown from a water–ethanol mixture (1:1 v/v).

Refinement top

H atoms were treated as riding atoms, with C—H distances of 0.95 (aromatic) or 0.99 Å (CH2) and N—H distances of 0.84 (for N4—H4) or 0.88 Å (NH2). An initial data set was collected at 120 (2) on a KappaCCD diffractometer using Mo Kα radiation. While it was possible to achieve a satisfactory description of the molecular and supramolecular structures from these data, from a refinement to R = 0.059 (wR = 0.153), the proportion of data labelled observed, even at 120 K, was only 0.48, and the average value of σ(C—C) was 0.012 Å. We therefore collected a second data set, at 150 (2) K, at the Daresbury synchrotron radiation source station 9.8 (Cernik et al., 1997; Clegg et al., 1998), and the proportion of data labelled observed rose to 0.69 and the refinement gave a mean σ(C—C) of only 0.003 Å. The greatly enhanced quality of the synchrotron data set may be significant for compounds of this type; as noted earlier (Quesada, Marchal et al., 2002), it is not always a straightforward matter to obtain crystals of substituted 5-nitrosopyrimidines suitable for single-crystal X-ray diffraction analysis and, indeed, some compounds of this type cannot be obtained in crystalline form at all. It seems clear that for some compounds of this series conventional diffactometry at ambient temperature would be fruitless and even CCD data at 120 K can lead to structural refinements of, at best, questionable acceptability.

Computing details top

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 1998); program(s) used to refine structure: SHELXTL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2002); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

Figures top
[Figure 1] Fig. 1. View of the molecule of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. Part of the crystal structure of (I), showing the formation of a chain along [001]. Atoms marked with an asterisk (*) or hash (#) are at the symmetry positions (x, y, 1 + z) and (x, y, -1 + z), respectively.
[Figure 3] Fig. 3. Part of the crystal structure of (I), showing the ππ-stacking interaction which links the [001] chains. Atoms marked with an asterisk (*) are at the symmetry position (-x, 1 - y, 1 - z).
4-(Allylamino)-2-amino-6-benzyloxy-5-nitrosopyrimidine top
Crystal data top
C14H15N5O2F(000) = 600
Mr = 285.31Dx = 1.351 Mg m3
Monoclinic, P21/cSynchrotron radiation, λ = 0.6867 Å
Hall symbol: -P 2ybcCell parameters from 2791 reflections
a = 8.0338 (6) Åθ = 2.6–25.4°
b = 24.627 (2) ŵ = 0.10 mm1
c = 7.4087 (5) ÅT = 150 K
β = 106.872 (2)°Plate, purple
V = 1402.7 (2) Å30.08 × 0.04 × 0.01 mm
Z = 4
Data collection top
Bruker SMART 1K CCD
diffractometer
2791 independent reflections
Radiation source: Daresbury SRS station 9.81931 reflections with I > 2σ(I)
Silicon 111 monochromatorRint = 0.038
ω rotation scans with narrow framesθmax = 25.4°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 109
Tmin = 0.992, Tmax = 0.999k = 2830
7631 measured reflectionsl = 99
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)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.125H-atom parameters constrained
S = 1.03 w = 1/[σ2(Fo2) + (0.0633P)2 + 0.1705P]
where P = (Fo2 + 2Fc2)/3
2791 reflections(Δ/σ)max < 0.001
190 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = 0.27 e Å3
Crystal data top
C14H15N5O2V = 1402.7 (2) Å3
Mr = 285.31Z = 4
Monoclinic, P21/cSynchrotron radiation, λ = 0.6867 Å
a = 8.0338 (6) ŵ = 0.10 mm1
b = 24.627 (2) ÅT = 150 K
c = 7.4087 (5) Å0.08 × 0.04 × 0.01 mm
β = 106.872 (2)°
Data collection top
Bruker SMART 1K CCD
diffractometer
2791 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
1931 reflections with I > 2σ(I)
Tmin = 0.992, Tmax = 0.999Rint = 0.038
7631 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0470 restraints
wR(F2) = 0.125H-atom parameters constrained
S = 1.03Δρmax = 0.17 e Å3
2791 reflectionsΔρmin = 0.27 e Å3
190 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.3161 (2)0.46034 (7)0.5285 (2)0.0309 (4)
N20.2980 (2)0.47602 (7)0.8268 (2)0.0389 (4)
C20.2614 (3)0.49352 (8)0.6499 (2)0.0306 (4)
N30.1769 (2)0.54067 (6)0.6094 (2)0.0304 (4)
N40.0524 (2)0.60415 (7)0.3854 (2)0.0345 (4)
C40.1377 (2)0.55755 (8)0.4302 (2)0.0280 (4)
C50.1880 (2)0.52673 (7)0.2880 (2)0.0276 (4)
N50.1612 (2)0.53997 (7)0.1038 (2)0.0325 (4)
O50.07881 (19)0.58396 (6)0.04541 (18)0.0381 (4)
O60.32262 (18)0.44649 (5)0.22616 (17)0.0317 (3)
C60.2778 (2)0.47725 (7)0.3543 (2)0.0278 (4)
C70.0030 (3)0.63751 (9)0.5207 (3)0.0410 (5)
C80.0868 (3)0.69082 (10)0.5583 (3)0.0498 (6)
C90.2027 (4)0.70983 (11)0.4840 (4)0.0651 (7)
C670.4035 (3)0.39442 (8)0.2922 (3)0.0344 (5)
C610.4135 (3)0.36349 (8)0.1208 (3)0.0308 (4)
C620.5526 (3)0.37115 (8)0.0485 (3)0.0352 (5)
C630.5595 (3)0.34374 (9)0.1137 (3)0.0414 (5)
C640.4301 (3)0.30761 (9)0.2002 (3)0.0455 (6)
C650.2915 (3)0.29946 (9)0.1286 (3)0.0460 (6)
C660.2818 (3)0.32760 (9)0.0314 (3)0.0388 (5)
H2A0.26670.49530.91140.058*
H2B0.35370.44510.85930.058*
H40.02890.61220.27060.041*
H7A0.01930.61730.64100.061*
H7B0.12990.64380.47200.061*
H80.05590.71360.64680.075*
H9A0.23870.68880.39460.098*
H9B0.25140.74480.51920.098*
H67A0.33300.37420.35930.052*
H67B0.52150.40000.37980.052*
H620.64380.39520.10980.042*
H630.65360.35000.16460.050*
H640.43620.28830.30910.055*
H650.20230.27460.18860.055*
H660.18540.32220.07920.047*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0421 (9)0.0335 (9)0.0188 (8)0.0002 (7)0.0116 (7)0.0006 (6)
N20.0601 (11)0.0406 (10)0.0179 (8)0.0053 (8)0.0143 (8)0.0025 (7)
C20.0391 (11)0.0364 (11)0.0177 (9)0.0062 (9)0.0106 (8)0.0014 (8)
N30.0401 (9)0.0328 (9)0.0201 (8)0.0030 (7)0.0117 (7)0.0017 (6)
N40.0484 (10)0.0350 (9)0.0236 (8)0.0032 (8)0.0160 (7)0.0006 (7)
C40.0342 (10)0.0296 (10)0.0222 (9)0.0058 (8)0.0111 (8)0.0016 (7)
C50.0342 (10)0.0304 (10)0.0197 (9)0.0046 (8)0.0101 (8)0.0015 (7)
N50.0421 (9)0.0347 (9)0.0221 (8)0.0020 (8)0.0116 (7)0.0031 (7)
O50.0514 (9)0.0386 (8)0.0255 (7)0.0045 (7)0.0128 (6)0.0070 (6)
O60.0482 (8)0.0304 (7)0.0197 (6)0.0045 (6)0.0148 (6)0.0014 (5)
C60.0357 (10)0.0316 (10)0.0182 (9)0.0040 (8)0.0113 (8)0.0024 (7)
C70.0509 (13)0.0438 (12)0.0333 (11)0.0101 (10)0.0202 (10)0.0014 (9)
C80.0579 (15)0.0463 (13)0.0459 (13)0.0059 (11)0.0163 (12)0.0142 (11)
C90.0787 (19)0.0516 (16)0.0684 (18)0.0173 (14)0.0269 (15)0.0173 (13)
C670.0463 (12)0.0348 (11)0.0259 (10)0.0066 (9)0.0163 (9)0.0041 (8)
C610.0392 (11)0.0301 (10)0.0231 (9)0.0047 (8)0.0092 (8)0.0028 (7)
C620.0397 (11)0.0369 (11)0.0302 (11)0.0005 (9)0.0119 (9)0.0060 (8)
C630.0471 (13)0.0457 (13)0.0354 (12)0.0035 (10)0.0181 (10)0.0079 (10)
C640.0614 (15)0.0426 (13)0.0297 (11)0.0043 (11)0.0088 (10)0.0091 (9)
C650.0537 (14)0.0404 (13)0.0373 (12)0.0058 (10)0.0029 (11)0.0063 (10)
C660.0417 (12)0.0395 (11)0.0345 (11)0.0008 (9)0.0100 (9)0.0044 (9)
Geometric parameters (Å, º) top
N1—C21.378 (2)C7—H7B0.990
C2—N31.335 (2)C8—H80.9500
N3—C41.339 (2)C9—H9A0.9500
C4—C51.448 (2)C9—H9B0.9500
C5—C61.429 (3)C67—C611.503 (3)
C6—N11.305 (2)C67—H67A0.990
C2—N21.329 (2)C67—H67B0.990
C4—N41.329 (2)C61—C621.385 (3)
N4—C71.462 (2)C61—C661.390 (3)
C7—C81.485 (3)C62—C631.393 (3)
C8—C91.298 (3)C62—H620.950
C5—N51.358 (2)C63—C641.377 (3)
N5—O51.278 (2)C63—H630.950
O6—C61.343 (2)C64—C651.380 (3)
O6—C671.457 (2)C64—H640.950
N2—H2A0.880C65—C661.395 (3)
N2—H2B0.880C65—H650.950
N4—H40.840C66—H660.950
C7—H7A0.990
C6—N1—C2115.32 (16)C9—C8—H8116.2
C2—N2—H2A120.0C7—C8—H8116.2
C2—N2—H2B120.0C8—C9—H9A120.0
H2A—N2—H2B120.0C8—C9—H9B120.0
N2—C2—N3117.15 (17)H9A—C9—H9B120.0
N2—C2—N1115.46 (18)O6—C67—C61106.87 (15)
N3—C2—N1127.38 (16)O6—C67—H67A110.3
C2—N3—C4116.80 (15)C61—C67—H67A110.3
C4—N4—C7123.50 (16)O6—C67—H67B110.3
C4—N4—H4114.0C61—C67—H67B110.3
C7—N4—H4122.5H67A—C67—H67B108.6
N4—C4—N3118.14 (16)C62—C61—C66119.34 (18)
N4—C4—C5120.26 (16)C62—C61—C67120.31 (18)
N3—C4—C5121.60 (17)C66—C61—C67120.34 (18)
N5—C5—C6117.88 (16)C61—C62—C63120.41 (19)
N5—C5—C4127.51 (17)C61—C62—H62119.8
C6—C5—C4114.61 (15)C63—C62—H62119.8
O5—N5—C5117.33 (15)C64—C63—C62120.0 (2)
C6—O6—C67116.36 (13)C64—C63—H63120.0
N1—C6—O6118.98 (17)C62—C63—H63120.0
N1—C6—C5124.27 (16)C63—C64—C65120.0 (2)
O6—C6—C5116.74 (15)C63—C64—H64120.0
N4—C7—C8113.42 (18)C65—C64—H64120.0
N4—C7—H7A108.9C64—C65—C66120.3 (2)
C8—C7—H7A108.9C64—C65—H65119.8
N4—C7—H7B108.9C66—C65—H65119.8
C8—C7—H7B108.9C61—C66—C65119.9 (2)
H7A—C7—H7B107.7C61—C66—H66120.0
C9—C8—C7127.5 (2)C65—C66—H66120.0
C4—C5—N5—O51.7 (3)N1—C6—O6—C673.3 (2)
N3—C4—N4—C70.9 (3)C6—O6—C67—C61170.4 (2)
C4—N4—C7—C8113.9 (2)O6—C67—C61—C6285.5 (2)
N4—C7—C8—C90.9 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4···O50.841.952.636 (2)138
N2—H2A···N5i0.882.163.035 (2)174
N2—H2A···O6i0.882.542.997 (2)113
N2—H2B···Cg2i0.882.813.655 (2)161
Symmetry code: (i) x, y, z+1.

Experimental details

Crystal data
Chemical formulaC14H15N5O2
Mr285.31
Crystal system, space groupMonoclinic, P21/c
Temperature (K)150
a, b, c (Å)8.0338 (6), 24.627 (2), 7.4087 (5)
β (°) 106.872 (2)
V3)1402.7 (2)
Z4
Radiation typeSynchrotron, λ = 0.6867 Å
µ (mm1)0.10
Crystal size (mm)0.08 × 0.04 × 0.01
Data collection
DiffractometerBruker SMART 1K CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.992, 0.999
No. of measured, independent and
observed [I > 2σ(I)] reflections
7631, 2791, 1931
Rint0.038
(sin θ/λ)max1)0.625
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.125, 1.03
No. of reflections2791
No. of parameters190
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.17, 0.27

Computer programs: SMART (Bruker, 1998), SAINT (Bruker, 2000), SAINT, SHELXTL (Sheldrick, 1998), SHELXTL and SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2002), SHELXL97 and PRPKAPPA (Ferguson, 1999).

Selected geometric parameters (Å, º) top
N1—C21.378 (2)N4—C71.462 (2)
C2—N31.335 (2)C7—C81.485 (3)
N3—C41.339 (2)C8—C91.298 (3)
C4—C51.448 (2)C5—N51.358 (2)
C5—C61.429 (3)N5—O51.278 (2)
C6—N11.305 (2)O6—C61.343 (2)
C2—N21.329 (2)O6—C671.457 (2)
C4—N41.329 (2)
C4—C5—N5—O51.7 (3)N1—C6—O6—C673.3 (2)
N3—C4—N4—C70.9 (3)C6—O6—C67—C61170.4 (2)
C4—N4—C7—C8113.9 (2)O6—C67—C61—C6285.5 (2)
N4—C7—C8—C90.9 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4···O50.841.952.636 (2)138
N2—H2A···N5i0.882.163.035 (2)174
N2—H2A···O6i0.882.542.997 (2)113
N2—H2B···Cg2i0.882.813.655 (2)161
Symmetry code: (i) x, y, z+1.
 

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