Malonamide: a tetra­gonal polymorph

Nichol, G.S.; Clegg, W.

doi:10.1107/S1600536805030539

organic compounds

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Volume 61| Part 10| October 2005| Pages o3424-o3426

doi:10.1107/S1600536805030539

Malonamide: a tetragonal polymorph

Gary S. Nichol ^a and William Clegg ^a ^*

^aSchool of Natural Sciences (Chemistry), Bedson Building, University of Newcastle, Newcastle upon Tyne NE1 7RU, England
^*Correspondence e-mail: w.clegg@ncl.ac.uk

(Received 21 September 2005; accepted 23 September 2005; online 28 September 2005)

A tetragonal polymorph of malonamide, C₃H₆N₂O₂, is reported. The unit-cell dimensions, crystallographic symmetry and some aspects of the molecular geometry are significantly different from those of the known monoclinic form [Chieh et al. (1970 ). J. Chem. Soc. A, pp. 179–184]. An R₃³(12) hydrogen-bonding motif links molecules together into a three-dimensional network.

Comment

Crystals of malonamide, (I), were obtained from a reaction between 4,6-dihydroxypyrimidine and Na₂CO₃ in water. Data collected at 150 K showed that it had crystallized in space group P4₃2₁2 with Z′ = 0.5 and Z = 4. It was only some time after structure solution that, by carrying out a search of the Cambridge Structural Database (CSD, Version 5.26; Allen, 2002 ), we realised a crystal structure of malonamide had previously been reported (Chieh et al., 1970) in space group P2₁/c with two independent molecules in the asymmetric unit and a final R = 0.05. This indicates either that the structure undergoes a phase transition above 150 K or that we had identified a second polymorph. However, by the time this was realized the original crystalline sample had been lost, although the original aqueous solution remained. In an attempt to answer this question we crystallized more of the product, with the intention of carrying out unit-cell determinations at 150 K and room temperature in order to show any phase transition. What we actually determined was a further, orthorhombic, polymorph of (I), described in the following paper (Nichol & Clegg, 2005 ). This third polymorph did not undergo a phase transition between room temperature and 150 K and, based on this observation, we are satisfied that the structure presented here is probably a genuine polymorph and not the consequence of a phase transition from the previously reported form as a result of cooling.

The molecular structure of (I) is shown in Fig. 1. The asymmetric unit consists of one half of the molecule, and the complete molecule is generated from the asymmetric unit by a twofold axis which passes through C2. Bond lengths and angles are in good agreement with the mean values reported by Chieh et al. (1970); however, the torsion angle about the C1—C2 bond is significantly different. Fig. 2 shows a wireframe diagram of (I) with two mean planes fitted through O, N, C1 and C2 and through the respective symmetry equivalents. Both planes intersect at C2 and the angle between the two planes is 58.68 (4)°. This value is over 27° less than the angles reported by Chieh et al. (1970) for both independent molecules (84.8 and 85.3°).

Fig. 3 shows a packing diagram viewed along the b axis. What initially looks like a complicated network is actually the result of just two independent N—H⋯O hydrogen bonds (one for each of the amino H atoms), with the O atom acting as a bifurcated acceptor. The result of this is a three-dimensional network of R₃³(12) hydrogen-bonding motifs, illustrated in Fig. 4 (Etter, 1990 ; Bernstein et al., 1995 ).

Figure 1
The molecular structure of (I)

, with displacement ellipsoids drawn at the 50% probability level and H atoms as small spheres. The labelled atoms indicate the asymmetric unit; the molecule is generated by a twofold rotation axis (y, x, −z) which passes through C2.

Figure 2
Two mean planes, one drawn through N, O, C1 and C2 and the other through their symmetry equivalents, and the dihedral angle between the two planes.

Figure 3
A packing diagram, viewed along the b axis. Hydrogen bonds are indicated by orange dashed lines.

Figure 4
The R₃³(12) hydrogen-bonding motif. Hydrogen bonds are indicated by orange dashed lines and C-bound H atoms are omitted.

Experimental

Equimolar amounts of 4,6-dihydroxypyrimidine and Na₂CO₃ were dissolved in 20 ml of hot distilled water, forming a pale-yellow solution. Large plate-shaped crystals of (I) were grown by slow evaporation of the cold solution on a watch glass over a period of approximately 5 d.

Crystal data

C₃H₆N₂O₂
M_r = 102.10
Tetragonal, P 4₃ 2₁ 2
a = 5.3140 (3) Å
c = 15.5360 (12) Å
V = 438.71 (5) Å³
Z = 4
D_x = 1.546 Mg m⁻³
Mo Kα radiation
Cell parameters from 54 reflections
θ = 2.5–27.5°
μ = 0.13 mm⁻¹
T = 150 (2) K
Plate, light yellow
0.50 × 0.50 × 0.02 mm

Data collection

Nonius KappaCCD diffractometer
φ and ω scans
Absorption correction: multi-scan(SADABS; Sheldrick, 2003 )T_min = 0.902, T_max = 0.997
6874 measured reflections
340 independent reflections
324 reflections with I > 2σ(I)
R_int = 0.018
θ_max = 27.5°
h = −6 → 6
k = −5 → 6
l = −20 → 20

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.032
wR(F²) = 0.082
S = 1.23
340 reflections
43 parameters
Only H-atom coordinates refined
w = 1/[σ²(F_o²) + (0.0509P)² + 0.0691P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.19 e Å⁻³
Δρ_min = −0.20 e Å⁻³
Extinction correction: SHELXL97
Extinction coefficient: 0.12 (3)

Table 1
Selected geometric parameters (Å, °)

O—C1	1.2382 (17)
N—C1	1.3251 (19)
C1—C2	1.5176 (17)

O—C1—C2—C1ⁱ	−36.66 (9)
N—C1—C2—C1ⁱ	145.23 (12)
Symmetry code: (i) y, x, -z.

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N—H1N⋯Oⁱⁱ	0.87 (2)	2.05 (2)	2.9195 (16)	171 (2)
N—H2N⋯Oⁱⁱⁱ	0.79 (2)	2.36 (2)	3.1112 (17)	158 (2)
Symmetry codes: (ii) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+{\script{1\over 4}}]$ ; (iii) y-1, x, -z.

All H atoms were located in a difference map and their coordinates were refined freely, with U_iso(H) = 1.2U_eq(N,C). The C—H bond length refined to 0.986 (19) Å and the two N—H bond lengths refined to 0.87 (2) and 0.79 (2) Å. Friedel pairs were merged during the final refinement cycles due to the lack of significant anomalous dispersion; the choice of chiral space group P4₃2₁2 rather than P4₁2₁2 is arbitrary.

Data collection: COLLECT (Nonius, 1998 ); cell refinement: DIRAX (Duisenberg, 1992 ); data reduction: EVALCCD (Duisenberg et al., 2003 ); program(s) used to solve structure: SIR2002 (Burla et al., 2003 ); program(s) used to refine structure: SHELXTL (Sheldrick, 2001 ); molecular graphics: DIAMOND3 (Brandenburg & Putz, 2004 ) and MERCURY (Version 1.3; Bruno et al., 2002 ); software used to prepare material for publication: SHELXTL and local programs.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536805030539/bt6745sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536805030539/bt6745Isup2.hkl

Comment top

Crystals of malonamide, (I), were obtained from a reaction between 4,6-dihydroxypyrimidine and Na₂CO₃ in water. Data collected at 150 K showed that it had crystallized in space group P4₃2₁2 with Z' = 0.5 and Z = 4. It was only some time after structure solution that, by carrying out a search of the Cambridge Structural Database (CSD, Version 5.26; Allen, 2002), we realised a crystal structure of malonamide had previously been reported (Chieh et al., 1970) in space group P2₁/c with two independent molecules in the asymmetric unit and a final R = 0.05. This indicates either that the structure undergoes a phase transition above 150 K or that we had identified a second polymorph. However, by the time this was realised the original crystalline sample had been lost, although the original aqueous solution remained. In an attempt to answer this question we crystallized more of the product, with the intention of carrying out unit-cell determinations at 150 K and room temperature in order to show any phase transition. What we actually determined was a further, orthorhombic, polymorph of (I), described in the following paper (Nichol & Clegg, 2005). This third polymorph did not undergo a phase transition between room temperature and 150 K and, based on this observation, we are satisfied that the structure presented here is probably a genuine polymorph and not the consequence of a phase transition from the previously reported form as a result of cooling.

Fig. 3 shows a packing diagram viewed along the b axis. What initially looks like a complicated network is actually the result of just two independent N—H···O hydrogen bonds (one for each of the amino H atoms), with the O atom acting as a bifurcated acceptor. The result of this is a three-dimensional network of R₃³(12) hydrogen-bonding motifs, illustrated in Fig. 4 (Etter, 1990; Bernstein et al., 1995).

Experimental top

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: DIRAX (Duisenberg, 1992); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2002 (Burla et al., 2003); program(s) used to refine structure: SHELXTL (Sheldrick, 2001); molecular graphics: DIAMOND3 (Brandenburg & Putz, 2004) and Mercury (Version 1.3; Bruno et al., 2002); software used to prepare material for publication: SHELXTL and local programs.

Figures top

	Fig. 1. The molecular structure of (I), with displacement ellipsoids drawn at the 50% probability level and H atoms as small spheres. The labelled atoms indicate the asymmetric unit; the molecule is generated by a twofold rotation axis (y, x, −z) which passes through C2.
	Fig. 2. Two mean planes, one drawn through N, O, C1 and C2 and the other through their symmetry equivalents, and the dihedral angle between the two planes.
	Fig. 3. A packing diagram, viewed along the b axis. Hydrogen bonds are indicated by orange dashed lines.
	Fig. 4. The R₃³(12) hydrogen-bonding motif. Hydrogen bonds are indicated by orange dashed lines and C-bound H atoms are omitted.

Malonamide top

Crystal data top

C₃H₆N₂O₂	D_x = 1.546 Mg m⁻³
M_r = 102.10	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, P4₃2₁2	Cell parameters from 54 reflections
Hall symbol: P 4nw 2abw	θ = 2.5–27.5°
a = 5.3140 (3) Å	µ = 0.13 mm⁻¹
c = 15.5360 (12) Å	T = 150 K
V = 438.71 (5) Å³	Block, light yellow
Z = 4	0.50 × 0.50 × 0.02 mm
F(000) = 216

Data collection top

Nonius KappaCCD diffractometer	340 independent reflections
Radiation source: sealed tube	324 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.018
ϕ and ω scans	θ_max = 27.5°, θ_min = 5.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −6→6
T_min = 0.902, T_max = 0.997	k = −5→6
6874 measured reflections	l = −20→20

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.032	Only H-atom coordinates refined
wR(F²) = 0.082	w = 1/[σ²(F_o²) + (0.0509P)² + 0.0691P] where P = (F_o² + 2F_c²)/3
S = 1.23	(Δ/σ)_max < 0.001
340 reflections	Δρ_max = 0.19 e Å⁻³
43 parameters	Δρ_min = −0.20 e Å⁻³
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.12 (3)

Crystal data top

C₃H₆N₂O₂	Z = 4
M_r = 102.10	Mo Kα radiation
Tetragonal, P4₃2₁2	µ = 0.13 mm⁻¹
a = 5.3140 (3) Å	T = 150 K
c = 15.5360 (12) Å	0.50 × 0.50 × 0.02 mm
V = 438.71 (5) Å³

Data collection top

Nonius KappaCCD diffractometer	340 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	324 reflections with I > 2σ(I)
T_min = 0.902, T_max = 0.997	R_int = 0.018
6874 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.032	0 restraints
wR(F²) = 0.082	Only H-atom coordinates refined
S = 1.23	Δρ_max = 0.19 e Å⁻³
340 reflections	Δρ_min = −0.20 e Å⁻³
43 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.

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

	x	y	z	U_iso*/U_eq
O	0.35135 (18)	0.5410 (2)	0.08252 (5)	0.0193 (4)
N	−0.0616 (2)	0.5402 (3)	0.04955 (8)	0.0182 (4)
H1N	−0.095 (4)	0.675 (4)	0.0800 (11)	0.022*
H2N	−0.177 (4)	0.469 (4)	0.0277 (12)	0.022*
C1	0.1676 (3)	0.4422 (3)	0.04704 (8)	0.0134 (4)
C2	0.1932 (2)	0.1932 (2)	0.0000	0.0147 (4)
H2	0.166 (3)	0.064 (4)	0.0448 (10)	0.018*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O	0.0154 (6)	0.0201 (6)	0.0222 (5)	−0.0024 (4)	−0.0014 (4)	−0.0069 (4)
N	0.0137 (7)	0.0158 (7)	0.0252 (7)	0.0002 (5)	−0.0013 (5)	−0.0063 (5)
C1	0.0148 (7)	0.0133 (7)	0.0121 (5)	−0.0017 (5)	0.0015 (5)	0.0008 (5)
C2	0.0130 (6)	0.0130 (6)	0.0180 (8)	−0.0020 (7)	0.0020 (5)	−0.0020 (5)

Geometric parameters (Å, º) top

O—C1	1.2382 (17)	N—C1	1.3251 (19)
N—H1N	0.87 (2)	C1—C2	1.5176 (17)
N—H2N	0.79 (2)	C2—H2	0.986 (19)

H1N—N—H2N	117 (2)	N—C1—C2	116.07 (11)
H1N—N—C1	121.7 (13)	C1—C2—C1ⁱ	112.84 (16)
H2N—N—C1	120.5 (15)	C1—C2—H2	104.6 (10)
O—C1—N	123.02 (13)	C1ⁱ—C2—H2	113.9 (11)
O—C1—C2	120.88 (12)

O—C1—C2—C1ⁱ	−36.66 (9)	N—C1—C2—C1ⁱ	145.23 (12)

Symmetry code: (i) y, x, −z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N—H1N···Oⁱⁱ	0.87 (2)	2.05 (2)	2.9195 (16)	170.8 (16)
N—H2N···Oⁱⁱⁱ	0.79 (2)	2.36 (2)	3.1112 (17)	157.6 (19)

Symmetry codes: (ii) x−1/2, −y+3/2, −z+1/4; (iii) y−1, x, −z.

Experimental details

Crystal data
Chemical formula	C₃H₆N₂O₂
M_r	102.10
Crystal system, space group	Tetragonal, P4₃2₁2
Temperature (K)	150
a, c (Å)	5.3140 (3), 15.5360 (12)
V (Å³)	438.71 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.13
Crystal size (mm)	0.50 × 0.50 × 0.02

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2003)
T_min, T_max	0.902, 0.997
No. of measured, independent and observed [I > 2σ(I)] reflections	6874, 340, 324
R_int	0.018
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.082, 1.23
No. of reflections	340
No. of parameters	43
H-atom treatment	Only H-atom coordinates refined
Δρ_max, Δρ_min (e Å⁻³)	0.19, −0.20

Computer programs: COLLECT (Nonius, 1998), DIRAX (Duisenberg, 1992), EVALCCD (Duisenberg et al., 2003), SIR2002 (Burla et al., 2003), SHELXTL (Sheldrick, 2001), DIAMOND3 (Brandenburg & Putz, 2004) and Mercury (Version 1.3; Bruno et al., 2002), SHELXTL and local programs.

Selected geometric parameters (Å, º) top

O—C1	1.2382 (17)	C1—C2	1.5176 (17)
N—C1	1.3251 (19)

O—C1—C2—C1ⁱ	−36.66 (9)	N—C1—C2—C1ⁱ	145.23 (12)

Symmetry code: (i) y, x, −z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N—H1N···Oⁱⁱ	0.87 (2)	2.05 (2)	2.9195 (16)	170.8 (16)
N—H2N···Oⁱⁱⁱ	0.79 (2)	2.36 (2)	3.1112 (17)	157.6 (19)

Symmetry codes: (ii) x−1/2, −y+3/2, −z+1/4; (iii) y−1, x, −z.

Acknowledgements

The authors thank the EPSRC for funding.

References

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Malonamide: a tetra­gonal polymorph

Comment

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

Malonamide: a tetragonal polymorph