N-(6-Bromo-4-oxo-3,4-di­hydro­pteridin-2-yl)-2,2-di­methyl­propan­amide

Shanmuga Sundara Raj, S.; Razak, I.A.; Fun, H.-K.; Goswami, S.; Mukherjee, R.; Adak, A.

doi:10.1107/S0108270100007861

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N-(6-Bromo-4-oxo-3,4-dihydropteridin-2-yl)-2,2-dimethylpropanamide

S. Shanmuga Sundara Raj, I. A. Razak, H.-K. Fun, S. Goswami, R. Mukherjee and A. Adak

In the title compound, C₁₁H₁₂BrN₅O₂, the rings in the pterin moiety are planar. The carbonyl O atom is in a synperiplanar conformation, while the C-N-C(=O)-C linkage is antiperiplanar. N-H

N and N-H

O intermolecular hydrogen bonds transform the molecules into infinite chains.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100007861/qa0311sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S0108270100007861/qa0311Isup2.hkl Contains datablock I

CCDC reference: 147697

Comment top

Pterin exist in polymeric structures, and folates having pterin moieties also exist as cyclic hydrogen-bonded tetramer which also forms a liquid-crystal mesophase (Mariani et al., 1989; Bonazzi et al., 1991). Almost all naturally occurring pterins (e.g. biopterin, neopterin, folic acid etc.) possess a substituent at the 6-position of the pterin ring. The difficulty in getting a single-crystal of pterin molecule is due to its notorious insolubility in common organic solvents and also in water. Introduction of a tert-butyl group (e.g. pivaloyl pterin) enhances its solubility by breaking the stronger hydrogen-bonded polymeric network arrangement of the pterin molecule. We report here the hydrogen-bonding network in the crystal structure of 2-pivaloyl-6-bromopterin, (I), as an example of a 6-substituted soluble pterin derivative.

The bond lengths and angles observed in the pterin moiety are comparable to the reported values (Nasir et al., 1992). The fused rings in the pterin moiety are planar, with the Br1 and O1 atoms deviating from the mean plane by −0.082 (1) and 0.132 (4) Å, respectively. The carbonyl O2 atom is in a synperiplanar conformation with respect to C5, while the conformation observed across the C5—N5—C7—C8 linkage is antiperiplanar. The geometry and conformational features resemble those of the chlorpterin derivative (Goswami et al., 2000). In the crystal, the N3 and N5 atoms are involved in N3—H3A···N4(x, 3/2 − y, −1/2 + z) and N5—H5A···O1(x, 3/2 − y, 1/2 + z) intermolecular hydrogen bonds. These hydrogen bonds form eight-membered hydrogen-bonded rings at each side of the molecules, each of which has the graph-set motif of R²₂(8) (Bernstein et al., 1995). These rings link the molecules into infinite chains in the [001] direction.

Experimental top

2-Amino-6-bromopterin (100 mg, 41 mmol) and 4-dimethylaminopyridine (10 mg) in pivalic anhydride (3 ml) were stirred at 353 K for 12 h. The excess pivalic anhydride and pivalic acid were removed carefully through short-path distillation under reduced pressure. The brown product was washed well with sodium carbonate (5% solution) followed by water and extracted with chloroform. The organic layer was evaporated under reduced pressure. The product was prepared by silica gel (60–120 mesh) eluting with 1% methanol in chloroform with yielded pure 2-pivaloylamino-6-bromopterin (120 mg, 90%). The compound was recrystallized from methylene chloride and methanol mixture (3:2 v/v)

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 1997); program(s) used to refine structure: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 1990).

N-(6-Bromo-4-oxo-3,4-dihydropteridin-2-yl)-2,2-dimethylpropanamide top

Crystal data top

C₁₁H₁₂BrN₅O₂	F(000) = 656
M_r = 326.17	D_x = 1.578 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 13.4315 (1) Å	Cell parameters from 4433 reflections
b = 10.3779 (2) Å	θ = 1.6–28.3°
c = 10.2560 (2) Å	µ = 3.00 mm⁻¹
β = 106.216 (1)°	T = 293 K
V = 1372.72 (4) Å³	Slab, yellow
Z = 4	0.36 × 0.26 × 0.22 mm

Data collection top

Siemens SMART CCD area-detector diffractometer	3332 independent reflections
Radiation source: fine-focus sealed tube	1999 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.067
Detector resolution: 8.33 pixels mm^-1	θ_max = 28.2°, θ_min = 1.6°
ω scans	h = −17→17
Absorption correction: empirical (using intensity measurements) (SADABS; Sheldrick, 1996)	k = −13→13
T_min = 0.381, T_max = 0.517	l = −13→12
9400 measured reflections

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)] = 0.054	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.128	H-atom parameters constrained
S = 0.94	w = 1/[σ²(F_o²) + (0.0873P)²] where P = (F_o² + 2F_c²)/3
3332 reflections	(Δ/σ)_max < 0.001
200 parameters	Δρ_max = 0.76 e Å⁻³
0 restraints	Δρ_min = −0.91 e Å⁻³

Crystal data top

C₁₁H₁₂BrN₅O₂	V = 1372.72 (4) Å³
M_r = 326.17	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 13.4315 (1) Å	µ = 3.00 mm⁻¹
b = 10.3779 (2) Å	T = 293 K
c = 10.2560 (2) Å	0.36 × 0.26 × 0.22 mm
β = 106.216 (1)°

Data collection top

Siemens SMART CCD area-detector diffractometer	3332 independent reflections
Absorption correction: empirical (using intensity measurements) (SADABS; Sheldrick, 1996)	1999 reflections with I > 2σ(I)
T_min = 0.381, T_max = 0.517	R_int = 0.067
9400 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.054	0 restraints
wR(F²) = 0.128	H-atom parameters constrained
S = 0.94	Δρ_max = 0.76 e Å⁻³
3332 reflections	Δρ_min = −0.91 e Å⁻³
200 parameters

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

	x	y	z	U_iso*/U_eq	Occ. (<1)
Br1	0.48346 (4)	0.19108 (5)	0.57471 (6)	0.0681 (2)
O1	0.2784 (3)	0.5192 (3)	0.1540 (2)	0.0566 (8)
O2	0.1154 (2)	0.8877 (3)	0.1507 (3)	0.0544 (8)
N1	0.3595 (3)	0.5396 (3)	0.6380 (3)	0.0462 (8)
N2	0.3757 (3)	0.3971 (4)	0.4093 (4)	0.0568 (9)
N3	0.2455 (2)	0.6974 (3)	0.2649 (3)	0.0331 (7)
H3A	0.2230	0.7383	0.1894	0.040*
N4	0.2759 (2)	0.7073 (3)	0.5022 (3)	0.0352 (7)
N5	0.2040 (2)	0.8812 (3)	0.3733 (3)	0.0329 (6)
H5A	0.2207	0.9259	0.4469	0.040*
C1	0.4061 (3)	0.4259 (4)	0.6502 (4)	0.0472 (10)
H1A	0.4342	0.3934	0.7373	0.057*
C2	0.4159 (3)	0.3520 (4)	0.5413 (4)	0.0394 (9)
C3	0.3267 (3)	0.5175 (3)	0.3960 (3)	0.0296 (7)
C4	0.2828 (3)	0.5739 (3)	0.2617 (3)	0.0339 (8)
C5	0.2428 (2)	0.7576 (3)	0.3817 (3)	0.0282 (7)
C6	0.3210 (3)	0.5871 (3)	0.5104 (3)	0.0320 (7)
C7	0.1408 (3)	0.9415 (4)	0.2590 (4)	0.0366 (8)
C8	0.1043 (3)	1.0784 (4)	0.2793 (4)	0.0476 (10)
C9A	0.0374 (8)	1.0643 (9)	0.3888 (11)	0.069 (4)	0.524 (12)
H9AA	−0.0170	1.0025	0.3562	0.103*	0.524 (12)
H9AB	0.0077	1.1462	0.4003	0.103*	0.524 (12)
H9AC	0.0820	1.0360	0.4743	0.103*	0.524 (12)
C10A	0.1933 (12)	1.1656 (13)	0.3428 (17)	0.072 (4)	0.524 (12)
H10A	0.2372	1.1252	0.4224	0.108*	0.524 (12)
H10B	0.1674	1.2454	0.3677	0.108*	0.524 (12)
H10C	0.2323	1.1821	0.2792	0.108*	0.524 (12)
C11A	0.0315 (12)	1.1274 (11)	0.1565 (10)	0.083 (5)	0.524 (12)
H11A	−0.0192	1.0623	0.1188	0.124*	0.524 (12)
H11B	0.0682	1.1496	0.0916	0.124*	0.524 (12)
H11C	−0.0026	1.2025	0.1780	0.124*	0.524 (12)
C9B	−0.0072 (10)	1.0720 (14)	0.2468 (18)	0.103 (6)	0.476 (12)
H9BA	−0.0340	1.0290	0.1613	0.155*	0.476 (12)
H9BB	−0.0350	1.1577	0.2410	0.155*	0.476 (12)
H9BC	−0.0267	1.0251	0.3165	0.155*	0.476 (12)
C10B	0.1625 (18)	1.1444 (15)	0.4029 (17)	0.099 (7)	0.476 (12)
H10D	0.2354	1.1374	0.4119	0.149*	0.476 (12)
H10E	0.1474	1.1055	0.4801	0.149*	0.476 (12)
H10F	0.1431	1.2337	0.3977	0.149*	0.476 (12)
C11B	0.1296 (18)	1.1592 (11)	0.1537 (16)	0.105 (6)	0.476 (12)
H11D	0.2030	1.1733	0.1737	0.158*	0.476 (12)
H11E	0.0944	1.2407	0.1431	0.158*	0.476 (12)
H11F	0.1062	1.1106	0.0711	0.158*	0.476 (12)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.0584 (3)	0.0535 (3)	0.0895 (5)	0.0152 (2)	0.0159 (3)	0.0327 (2)
O1	0.106 (2)	0.0400 (16)	0.0206 (13)	0.0180 (15)	0.0121 (14)	−0.0003 (11)
O2	0.0705 (19)	0.0516 (17)	0.0274 (14)	0.0188 (14)	−0.0088 (13)	−0.0049 (12)
N1	0.063 (2)	0.049 (2)	0.0204 (15)	0.0008 (16)	0.0022 (15)	0.0081 (13)
N2	0.060 (2)	0.048 (2)	0.060 (2)	0.0016 (17)	0.0115 (19)	0.0118 (17)
N3	0.0508 (18)	0.0318 (16)	0.0146 (14)	0.0044 (12)	0.0057 (12)	0.0031 (11)
N4	0.0521 (18)	0.0367 (17)	0.0166 (14)	0.0020 (13)	0.0095 (13)	0.0012 (11)
N5	0.0459 (17)	0.0315 (16)	0.0190 (14)	0.0036 (13)	0.0050 (12)	−0.0057 (11)
C1	0.052 (2)	0.051 (2)	0.029 (2)	0.0004 (18)	−0.0040 (17)	0.0139 (18)
C2	0.0335 (19)	0.038 (2)	0.043 (2)	0.0010 (15)	0.0034 (16)	0.0170 (16)
C3	0.0355 (18)	0.0314 (18)	0.0210 (16)	−0.0010 (13)	0.0064 (14)	0.0019 (13)
C4	0.049 (2)	0.0324 (18)	0.0176 (16)	0.0024 (15)	0.0045 (14)	0.0005 (13)
C5	0.0317 (17)	0.0336 (18)	0.0198 (17)	−0.0027 (14)	0.0077 (13)	−0.0022 (13)
C6	0.0373 (18)	0.0361 (19)	0.0221 (16)	−0.0027 (14)	0.0074 (14)	0.0044 (14)
C7	0.039 (2)	0.041 (2)	0.0260 (18)	0.0040 (15)	0.0037 (15)	−0.0002 (15)
C8	0.051 (2)	0.038 (2)	0.045 (2)	0.0102 (17)	−0.0005 (19)	−0.0035 (17)
C9A	0.078 (7)	0.059 (6)	0.080 (8)	0.020 (5)	0.038 (6)	−0.008 (5)
C10A	0.075 (7)	0.036 (6)	0.103 (13)	−0.008 (5)	0.021 (8)	−0.012 (7)
C11A	0.128 (12)	0.055 (7)	0.047 (6)	0.045 (7)	−0.004 (7)	0.000 (5)
C9B	0.078 (9)	0.092 (11)	0.139 (19)	0.028 (8)	0.030 (10)	−0.006 (10)
C10B	0.16 (2)	0.035 (8)	0.082 (12)	0.028 (10)	−0.008 (10)	−0.015 (7)
C11B	0.184 (18)	0.048 (7)	0.111 (11)	0.033 (9)	0.086 (12)	0.038 (7)

Geometric parameters (Å, º) top

Br1—C2	1.886 (4)	N5—C7	1.390 (4)
O1—C4	1.228 (4)	C1—C2	1.391 (6)
O2—C7	1.204 (4)	C3—C6	1.398 (4)
N1—C1	1.325 (5)	C3—C4	1.461 (4)
N1—C6	1.358 (4)	C7—C8	1.536 (5)
N2—C2	1.391 (5)	C8—C9B	1.441 (13)
N2—C3	1.401 (5)	C8—C11A	1.453 (9)
N3—C5	1.361 (4)	C8—C10B	1.461 (18)
N3—C4	1.379 (4)	C8—C10A	1.496 (15)
N4—C5	1.301 (4)	C8—C9A	1.629 (10)
N4—C6	1.380 (4)	C8—C11B	1.651 (12)
N5—C5	1.378 (4)

C1—N1—C6	117.2 (3)	N5—C7—C8	116.4 (3)
C2—N2—C3	116.0 (3)	C9B—C8—C11A	54.0 (8)
C5—N3—C4	123.2 (3)	C9B—C8—C10B	119.5 (11)
C5—N4—C6	116.7 (3)	C11A—C8—C10B	131.0 (8)
C5—N5—C7	127.1 (3)	C9B—C8—C10A	141.3 (8)
N1—C1—C2	124.2 (3)	C11A—C8—C10A	115.4 (9)
N2—C2—C1	119.9 (3)	C10B—C8—C10A	33.8 (8)
N2—C2—Br1	120.7 (3)	C9B—C8—C7	106.0 (6)
C1—C2—Br1	119.4 (3)	C11A—C8—C7	111.6 (5)
C6—C3—N2	120.9 (3)	C10B—C8—C7	115.9 (7)
C6—C3—C4	118.8 (3)	C10A—C8—C7	111.8 (6)
N2—C3—C4	120.3 (3)	C9B—C8—C9A	54.4 (7)
O1—C4—N3	121.6 (3)	C11A—C8—C9A	105.2 (8)
O1—C4—C3	124.6 (3)	C10B—C8—C9A	73.1 (10)
N3—C4—C3	113.8 (3)	C10A—C8—C9A	106.4 (7)
N4—C5—N3	124.5 (3)	C7—C8—C9A	105.6 (4)
N4—C5—N5	117.1 (3)	C9B—C8—C11B	105.7 (11)
N3—C5—N5	118.4 (3)	C11A—C8—C11B	51.8 (8)
N1—C6—N4	115.4 (3)	C10B—C8—C11B	105.2 (10)
N1—C6—C3	121.7 (3)	C10A—C8—C11B	73.7 (9)
N4—C6—C3	122.8 (3)	C7—C8—C11B	102.8 (5)
O2—C7—N5	121.2 (3)	C9A—C8—C11B	149.0 (7)
O2—C7—C8	122.4 (3)

C6—N1—C1—C2	−1.5 (6)	C5—N4—C6—N1	176.9 (3)
C3—N2—C2—C1	−0.1 (5)	C5—N4—C6—C3	−3.5 (5)
C3—N2—C2—Br1	179.8 (3)	N2—C3—C6—N1	−2.1 (5)
N1—C1—C2—N2	0.4 (6)	C4—C3—C6—N1	179.4 (3)
N1—C1—C2—Br1	−179.4 (3)	N2—C3—C6—N4	178.3 (3)
C2—N2—C3—C6	0.9 (5)	C4—C3—C6—N4	−0.2 (5)
C2—N2—C3—C4	179.4 (3)	C5—N5—C7—O2	−1.9 (6)
C5—N3—C4—O1	175.4 (3)	C5—N5—C7—C8	177.3 (3)
C5—N3—C4—C3	−4.7 (5)	O2—C7—C8—C9B	61.3 (9)
C6—C3—C4—O1	−176.0 (4)	N5—C7—C8—C9B	−117.8 (8)
N2—C3—C4—O1	5.5 (6)	O2—C7—C8—C11A	4.2 (9)
C6—C3—C4—N3	4.1 (5)	N5—C7—C8—C11A	−174.8 (8)
N2—C3—C4—N3	−174.4 (3)	O2—C7—C8—C10B	−163.5 (11)
C6—N4—C5—N3	3.2 (5)	N5—C7—C8—C10B	17.4 (11)
C6—N4—C5—N5	−175.7 (3)	O2—C7—C8—C10A	−126.7 (7)
C4—N3—C5—N4	1.1 (5)	N5—C7—C8—C10A	54.2 (8)
C4—N3—C5—N5	180.0 (3)	O2—C7—C8—C9A	118.0 (6)
C7—N5—C5—N4	−161.7 (3)	N5—C7—C8—C9A	−61.1 (6)
C7—N5—C5—N3	19.4 (5)	O2—C7—C8—C11B	−49.4 (9)
C1—N1—C6—N4	−178.1 (3)	N5—C7—C8—C11B	131.5 (9)
C1—N1—C6—C3	2.3 (5)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···O2	0.86	2.08	2.680 (4)	126
N3—H3A···N4ⁱ	0.86	2.30	3.003 (4)	140
N5—H5A···O1ⁱⁱ	0.86	2.13	2.958 (4)	163

Symmetry codes: (i) x, −y+3/2, z−1/2; (ii) x, −y+3/2, z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₁H₁₂BrN₅O₂
M_r	326.17
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	13.4315 (1), 10.3779 (2), 10.2560 (2)
β (°)	106.216 (1)
V (Å³)	1372.72 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	3.00
Crystal size (mm)	0.36 × 0.26 × 0.22

Data collection
Diffractometer	Siemens SMART CCD area-detector diffractometer
Absorption correction	Empirical (using intensity measurements) (SADABS; Sheldrick, 1996)
T_min, T_max	0.381, 0.517
No. of measured, independent and observed [I > 2σ(I)] reflections	9400, 3332, 1999
R_int	0.067
(sin θ/λ)_max (Å⁻¹)	0.665

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.054, 0.128, 0.94
No. of reflections	3332
No. of parameters	200
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.76, −0.91

Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SAINT, SHELXTL (Sheldrick, 1997), SHELXTL and PLATON (Spek, 1990).

Selected geometric parameters (Å, º) top

Br1—C2	1.886 (4)	N3—C5	1.361 (4)
O1—C4	1.228 (4)	N3—C4	1.379 (4)
O2—C7	1.204 (4)	N4—C5	1.301 (4)
N1—C1	1.325 (5)	N4—C6	1.380 (4)
N1—C6	1.358 (4)	N5—C5	1.378 (4)
N2—C2	1.391 (5)	N5—C7	1.390 (4)
N2—C3	1.401 (5)

C5—N5—C7	127.1 (3)	O2—C7—C8	122.4 (3)
O2—C7—N5	121.2 (3)	N5—C7—C8	116.4 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···O2	0.86	2.08	2.680 (4)	126
N3—H3A···N4ⁱ	0.86	2.30	3.003 (4)	140
N5—H5A···O1ⁱⁱ	0.86	2.13	2.958 (4)	163

Symmetry codes: (i) x, −y+3/2, z−1/2; (ii) x, −y+3/2, z+1/2.

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N-(6-Bromo-4-oxo-3,4-di­hydro­pteridin-2-yl)-2,2-di­methyl­propan­amide

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N-(6-Bromo-4-oxo-3,4-dihydropteridin-2-yl)-2,2-dimethylpropanamide