Malonamide: an ortho­rhom­bic polymorph

An ortho­rhom­bic 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] and of the tetra­gonal form described in the previous paper [Nichol & Clegg (2005). Acta Cryst. E61, o3424–o3426]. A simple R₄²(8) motif links the mol­ecules together and the symmetry of the mol­ecule means that this extends into a three-dimensional network.

Comment

In the previous paper (Nichol & Clegg, 2005), we reported a tetra­gonal polymorph of malonamide, (I). By crystallizing a second sample from the original reaction solution we have obtained a further polymorph, this time in the ortho­rhom­bic crystal system. The only previously known polymorph of malonamide (Chieh et al., 1970) was reported in the space group P2₁/c at room temperature, with two independent mol­ecules in the asymmetric unit and a final R = 0.05. After realizing that we had identified a second crystalline form of this compound, we wished to redetermine the unit cell at room temperature in order to establish whether this was a temperature-induced phase transition or a completely new polymorph stable under the same conditions. To do this we had to recrystallize the sample again and what we actually obtained was (I) as yet another, ortho­rhom­bic, polymorph.

The mol­ecular structure of (I) is shown in Fig. 1. The asymmetric unit consists of one half of the mol­ecule, the complete mol­ecule being generated by a twofold rotation axis which passes through C2. Bond lengths and angles are in good agreement with the mean values for the other polymorphs and the dihedral angle between the O/N/C1/C2 mean plane and its symmetry equivalent (Fig. 2), at 71.90 (4)°, is much closer to the values calculated from the report of Chieh et al. (1970) for their two independent mol­ecules (84.8 and 85.3°) than is the case with the tetra­gonal polymorph [58.68 (4)°].

Fig. 3 shows a packing diagram viewed along the a axis. Both independent N—H bonds are involved in hydrogen bonding and each O atom is therefore a bifurcated acceptor. The hydrogen bonding consists of a simple R₄²(8) graph-set motif (Etter, 1990; Bernstein et al., 1995), illustrated in Fig. 4. The crystallographic rotation symmetry of the mol­ecule means that this simple motif extends into a complex three-dimensional network.

Intrigued by the newly discovered polymorphism of this compound, we have made numerous attempts to obtain again the tetra­gonal form. Despite carrying out the preparation and crystallization in different locations, we have always obtained the ortho­rhom­bic form (the third polymorph, described in this paper) and never one of the others, either monoclinic or tetra­gonal. We wonder whether this is an example of the phenomenon of `disappearing polymorphs' (Dunitz & Bernstein, 1995).

Figure 1 The mol­ecular structure of (I), with displacement ellipsoids drawn at the 50% probability level and hydrogen atoms as small spheres. The labelled atoms indicate the asymmetric unit; the complete mol­ecule is generated by a twofold rotation axis (−x, y, − 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 a axis. Hydrogen bonds are indicated by dashed orange lines.

Figure 4 The R4^2(8) motif; dashed orange lines indicate hydrogen bonding and C—H H atoms have been omitted.

Experimental

Equimolar amounts of 4,6-dihydroxy­pyrimidine and Na₂CO₃ were dissolved in 20 ml of hot distilled water, forming a pale-yellow solution, from which crystals of the tetra­gonal polymorph were initially obtained after several days (Nichol & Clegg, 2005). The solution was stored in a sealed container for several months. Large plate crystals of (I) were subsequently grown by evaporation of the cold solution on a watch glass over a period of a few hours.

Crystal data

• C₃H₆N₂O₂

• M_r = 102.10

• Orthorhombic, P b c n

• a = 5.3602 (9) Å

• b = 7.5178 (8) Å

• c = 11.791 (2) Å

• V = 475.14 (12) ų

• Z = 4

• D_x = 1.427 Mg m⁻³

• Mo Kα radiation

• Cell parameters from 6050 reflections

• θ = 2.5–27.5°

• μ = 0.12 mm⁻¹

• T = 150 (2) K

• Block cut from large plate, colourless

• 0.42 × 0.36 × 0.26 mm

Data collection

• Nonius KappaCCD diffractometer

• φ and ω scans

• Absorption correction: multi-scan(SADABS; Sheldrick, 2003)T_min = 0.911, T_max = 0.970

• 8872 measured reflections

• 539 independent reflections

• 490 reflections with I > 2σ(I)

• R_int = 0.021

• θ_max = 27.5°

• h = −6 → 6

• k = −9 → 9

• l = −15 → 15

Refinement

• Refinement on F²

• R[F² > 2σ(F²)] = 0.031

• wR(F²) = 0.083

• S = 1.11

• 539 reflections

• 43 parameters

• Only H-atom coordinates refined

• w = 1/[σ²(F_o²) + (0.0412P)² + 0.1866P] where P = (F_o² + 2F_c²)/3

• (Δ/σ)_max < 0.001

• Δρ_max = 0.31 e Å⁻³

• Δρ_min = −0.20 e Å⁻³

• Extinction correction: SHELXL97

• Extinction coefficient: 0.077 (17)

Table 1
Selected geometric parameters (Å, °)

O—C1	1.2420 (13)
N—C1	1.3257 (14)
C1—C2	1.5178 (13)

O—C1—C2—C1^i	−45.99 (8)
N—C1—C2—C1^i	134.54 (10)
Symmetry code: (i) .

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N—H1N⋯O^ii	0.89 (2)	2.06 (2)	2.9282 (13)	166 (1)
N—H2N⋯O^iii	0.85 (2)	2.12 (2)	2.9502 (14)	169 (2)
Symmetry codes: (ii) ; (iii) .

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 0.964 (13) Å and the two N—H bond lengths refined to 0.887 (16) and 0.846 (19) Å.

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

Supporting information

S1. Comment

In the previous paper (Nichol & Clegg, 2005), we reported a tetragonal polymorph of malonamide, (I). By crystallizing a second sample from the original reaction solution we have obtained a further polymorph, this time in the orthorhombic crystal system. The only previously known polymorph of malonamide (Chieh et al., 1970) was reported in the space group P2₁/c at room temperature, with two independent molecules in the asymmetric unit and a final R = 0.05. After realising that we had identified a second crystalline form of this compound, we wished to redetermine the unit cell at room temperature in order to establish whether this was a temperature-induced phase transition or a completely new polymorph stable under the same conditions. To do this we had to recrystallize the sample again and what we actually obtained was (I) as yet another, orthorhombic, polymorph.

The molecular structure of (I) is shown in Fig. 1. The asymmetric unit consists of one half of the molecule, the complete molecule being generated by a twofold rotation axis which passes through C2. Bond lengths and angles are in good agreement with the mean values for the other polymorphs and the dihedral angle between the O/N/C1/C2 mean plane and its symmetry equivalent (Fig. 2), at 71.90 (4)°, is much closer to the values calculated from the report of Chieh et al. (1970) for their two independent molecules (84.8 and 85.3°) than is the case with the tetragonal polymorph [58.68 (4)°].

Fig. 3 shows a packing diagram viewed along the a axis. Both independent N—H bonds are involved in hydrogen bonding and each O atom is therefore a bifurcated acceptor. The hydrogen bonding consists of a simple R₄²(8) graph-set motif (Etter, 1990; Bernstein et al., 1995), illustrated in Fig. 4. The crystallographic rotation symmetry of the molecule means that this simple motif extends into a complex three-dimensional network.

Intrigued by the newly discovered polymorphism of this compound, we have made numerous attempts to obtain again the tetragonal form. Despite carrying out the preparation and crystallization in different locations, we have always obtained the orthorhombic form (the third polymorph, described in this paper) and never one of the others, either monoclinic or tetragonal. We wonder whether this is an example of the phenomenon of `disappearing polymorphs' (Dunitz & Bernstein, 1995).

S2. Experimental

Equimolar amounts of 4,6-dihydroxypyrimidine and Na₂CO₃ were dissolved in 20 ml of hot distilled water, forming a pale-yellow solution, from which crystals of the tetragonal polymorph were initially obtained after several days (Nichol & Clegg, 2005). The solution was stored in a sealed container for several months. Large plate crystals of (I) were subsequently grown by evaporation of the cold solution on a watch glass over a period of a few hours.

S3. Refinement

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 0.964 (13) Å and the two N—H bond lengths refined to 0.887 (16) and 0.846 (19) Å.

Computing details

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

Figures

	Fig. 1. The molecular structure of (I), with displacement ellipsoids drawn at the 50% probability level and hydrogen atoms as small spheres. The labelled atoms indicate the asymmetric unit; the complete molecule is generated by a twofold rotation axis (−x, y, 1/2 − 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 a axis. Hydrogen bonds are indicated by dashed orange lines.
	Fig. 4. The R4^2(8) motif; dashed orange lines indicate hydrogen bonding and C—H H atoms have been omitted.

Malonamide

Crystal data

C3H6N2O2	F(000) = 216
Mr = 102.10	Dx = 1.427 Mg m^−3
Orthorhombic, Pbcn	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2n 2ab	Cell parameters from 6050 reflections
a = 5.3602 (9) Å	θ = 2.5–27.5°
b = 7.5178 (8) Å	µ = 0.12 mm^−1
c = 11.791 (2) Å	T = 150 K
V = 475.14 (12) Å^3	Block cut from large plate, colourless
Z = 4	0.42 × 0.36 × 0.26 mm

Data collection

Nonius KappaCCD diffractometer	539 independent reflections
Radiation source: sealed tube	490 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.021
ϕ and ω scans	θmax = 27.5°, θmin = 4.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −6→6
Tmin = 0.911, Tmax = 0.970	k = −9→9
8872 measured reflections	l = −15→15

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.031	Only H-atom coordinates refined
wR(F^2) = 0.083	w = 1/[σ^2(Fo^2) + (0.0412P)^2 + 0.1866P] where P = (Fo^2 + 2Fc^2)/3
S = 1.11	(Δ/σ)max < 0.001
539 reflections	Δρmax = 0.31 e Å^−3
43 parameters	Δρmin = −0.20 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.077 (17)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
O	0.06613 (15)	0.25831 (10)	0.37641 (7)	0.0222 (3)
N	−0.2702 (2)	0.08531 (14)	0.40865 (9)	0.0250 (3)
H1N	−0.313 (3)	0.1499 (19)	0.4686 (14)	0.030*
H2N	−0.355 (3)	−0.005 (3)	0.3895 (13)	0.030*
C1	−0.06739 (19)	0.12942 (13)	0.35078 (8)	0.0161 (3)
C2	0.0000	0.01335 (19)	0.2500	0.0161 (4)
H2	0.136 (3)	−0.0629 (16)	0.2721 (11)	0.019*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O	0.0269 (5)	0.0211 (5)	0.0187 (5)	−0.0057 (3)	0.0001 (3)	−0.0038 (3)
N	0.0295 (6)	0.0226 (5)	0.0228 (5)	−0.0060 (4)	0.0109 (4)	−0.0065 (4)
C1	0.0200 (5)	0.0152 (5)	0.0131 (5)	0.0013 (4)	−0.0008 (4)	0.0014 (3)
C2	0.0195 (7)	0.0142 (7)	0.0144 (6)	0.000	0.0012 (5)	0.000

Geometric parameters (Å, º)

O—C1	1.2420 (13)	N—C1	1.3257 (14)
N—H1N	0.887 (16)	C1—C2	1.5178 (13)
N—H2N	0.846 (19)	C2—H2	0.963 (13)
H1N—N—H2N	120.8 (15)	N—C1—C2	117.02 (9)
H1N—N—C1	119.0 (10)	C1—C2—C1^i	109.82 (12)
H2N—N—C1	120.1 (11)	C1—C2—H2	108.1 (8)
O—C1—N	122.85 (10)	C1^i—C2—H2	112.0 (8)
O—C1—C2	120.12 (9)
O—C1—C2—C1^i	−45.99 (8)	N—C1—C2—C1^i	134.54 (10)

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N—H1N···O^ii	0.887 (16)	2.058 (17)	2.9282 (13)	166.4 (13)
N—H2N···O^iii	0.846 (19)	2.116 (19)	2.9502 (14)	168.7 (15)

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