Crystal structure of 5-hy­droxy-5-propyl­barbituric acid

Gelbrich, T.; Griesser, U.J.

doi:10.1107/S2056989015018769

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Volume 71| Part 11| November 2015| Pages 1311-1314

https://doi.org/10.1107/S2056989015018769

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Crystal structure of 5-hydroxy-5-propylbarbituric acid

Thomas Gelbrich ^a ^* and Ulrich J. Griesser ^a

^aUniversity of Innsbruck, Institute of Pharmacy, Innrain 52, 6020 Innsbruck, Austria
^*Correspondence e-mail: thomas.gelbrich@uibk.ac.at

Edited by G. Smith, Queensland University of Technology, Australia (Received 8 September 2015; accepted 6 October 2015; online 14 October 2015)

Molecules of the title compound, C₇H₁₀N₂O₄, systematic name 5-hydroxy-5-propylpyrimidine-2,4,6(1H,3H,5H)-trione, form a hydrogen-bonded framework which is based on three independent hydrogen bonds, N—H⋯O(carbonyl), N—H⋯O(hydroxy) and O—H⋯O(carbonyl). This framework has the topology of the 5-connected nov net. Each molecule is linked to five other molecules via six hydrogen bonds, and the descriptor of the hydrogen-bonded structure is F6₅[4⁴.6⁶-nov]. The crystal packing is isostructural with that of the previously reported 5-hydroxy-5-ethyl analogue.

Keywords: barbiturates; crystal structure; hydrogen bonding; isostructurality; topology; XPac.

CCDC reference: 1429681

1. Chemical context

As part of a systematic investigation of solid-state properties of derivatives of barbituric acid (Gelbrich et al., 2015 ; Zencirci et al., 2014 ; Rossi et al., 2012 ), we are studying the polymorphism of a group of 5-monosubstituted barbituric acids. The title compound is an oxidation product of 5-propylbarbituric acid, formed during a crystallization experiment and the structure is reported herein. The analogous oxidation product of 5-ethylbarbituric acid was previously reported by Gatehouse & Craven (1971 ).

2. Structural commentary

The molecule of the title compound (Fig. 1) displays a pyrimidine ring (N1/C2/N3/C4/C5/C6) in a C5-envelope conformation. The ring puckering parameters calculated with PLATON (Spek, 2009 ) are θ = 134.4 (3), Φ = 52.2 (5)° and Q = 0.2420 (14) Å. The distance of C5 from the mean plane defined by the other four ring atoms [maximum deviation: N3; −0.033 (1) Å] is −0.342 (2) Å. At ring atom C5 the propyl substituent adopts a trans conformation, and the corresponding torsion angle C5—C8—C9—C10 is −164.80 (13)°. The C5—C8—C9—C10 fragment is twisted significantly out of the plane defined by atoms C8, C5 and C2, which bisects the pyrimidinetrione fragment into two approximately symmetrical halves, resulting in a pseudo-torsion angle C2⋯C5—C8—C9 of −125.69 (11)°. Closer inspection suggests that this particular geometry may help to prevent unfavourably close intramolecular contacts between the O7 hydroxy group and the CH₂ group at C9, and may be also facilitate the participation of the hydroxy group in complex intermolecular hydrogen-bonding interactions.

Figure 1
Asymmetric unit with displacement ellipsoids drawn at the 50% probability level and hydrogen atoms drawn as spheres of arbitrary size.

3. Supramolecular features

One NH group and one carbonyl group of the molecule are engaged in a centrosymmetric two-point interaction, N3—H3⋯O4ⁱⁱ (Table 1), resulting in an R₂²(8) ring (Etter et al., 1990 ; Bernstein et al., 1995 ). This kind of ring is a ubiquitous feature in crystal structures of barbiturates (Gelbrich et al., 2011 ). The other NH group is bonded to the hydroxy group of a second molecule via a 2₁ operation, N1—H1⋯O7ⁱ, and this interaction is accompanied by a short O6⋯C4ⁱ contact [2.8654 (18) Å]. Additionally, the hydroxy group donates a hydrogen bond to the C2 carbonyl group of another molecule related by glide symmetry (O7—H7⋯O2ⁱⁱⁱ). Altogether, six hydrogen bonds connect each molecule to five other molecules. In addition to the aforementioned R₂²(8) rings, the resulting hydrogen-bonded framework structure also displays rings composed of four and six molecules (Fig. 2). This 5-connected framework has the topology of the nov structure (Blatov et al., 2004 ). Fig. 3 shows a graph of the hydrogen-bonded structure (HBS) according to the methodology proposed by Hursthouse et al. (2015 ). The short descriptor according to Hursthouse et al. (2015) for this HBS is F6₅[4⁴.6⁶-nov].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O7ⁱ	0.87 (1)	2.03 (1)	2.8683 (17)	164 (2)
N3—H3⋯O4ⁱⁱ	0.86 (1)	2.00 (1)	2.8451 (16)	170 (2)
O7—H7⋯O2ⁱⁱⁱ	0.84 (2)	1.98 (2)	2.8055 (15)	169 (2)
Symmetry codes: (i) $[-x+{\script{3\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) -x+1, -y+2, -z+1; (iii) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ .

Figure 2
Layer fragment of the H-bonded framework which contains rings connecting four and six molecules in addition to R₂²(8) rings. Hydrogen bonds are drawn as dashed lines. H and O atoms engaged in hydrogen bonding are drawn as balls and all the other H atoms are omitted for clarity.

Figure 3
The N—H⋯O(carbonyl), N—H⋯O(hydroxy) and O—H⋯O(carbonyl) bonded F6₅[4⁴.6⁶-nov] structure of title compound. Molecules are represented as nodes and their hydrogen-bond connections as links between them.

4. Database survey

The Cambridge Structural Database (Version 5.36; Groom & Allen, 2014 ) contains the crystal structure of 5,5-dihydroxybarbituric acid (Singh, 1965 ; Harrowfield et al., 1989 ; CSD refcode ALXANM01) and those of a monohydrate (Lewis & Tocher, 2004 ; PAGYUS), a trihydrate (Lewis & Tocher, 2004b ; HBARBT01) and a 1,4-dioxane hemisolvate (Gelbrich et al., 2010 ; NUQYII) of the same compound. Two-point connections based on N—H⋯O=C bonds which result in characteristic R₂²(8) rings are found in each of these compounds.

The title structure displays just one such interaction which involves the carbonyl group at ring position 4 (Fig. 4). One such connection, albeit via the C2 carbonyl group, also exists in the 5,5-dihydroxybarbituric acid structure. Here it forms part of the C-4 ladder motif which is known from 5,5-disubstituted derivatives of barbituric acid (Gelbrich et al., 2011).

Figure 4
An illustration of the similar packing of molecules in the title compound (left) and its ethyl analogue (right). Each structure is viewed along its [010] direction. H atoms in alkyl groups are omitted for clarity.

The monohydrate and 1,4-dioxane hemisolvate each contain two two-point N—H⋯O=C connections per molecule, in the first case via the topologically equivalent C4 and C6 carbonyl groups and in the second via the C4 and C2 carbonyl groups, resulting in the looped chain motifs C-2 and C-1 (Gelbrich et al., 2011), respectively, which are frequently encountered in barbiturates. C-2 chains are also found in the structure of the trihydrate. The molecular conformation of 5-hydroxy-5-ethylbarbituric acid (Gatehouse & Craven, 1971; HEBARB) is similar to that of the title structure with respect to the pseudo-torsion angle of 124.3°, which is structurally analogous to the C2⋯C5—C8—C9 angle discussed above. A comparison with the program XPac (for details, see below) indicated that these two compounds are indeed isostructural. Geometrical differences between the two molecular packing arrangements are small (Fig. 4), which is reflected in a calculated XPac dissimilarity index of just 5.4. This close packing similarity is remarkable insofar as the substitution of a propyl with an ethyl group alters the molecular shape considerably and leads to an 11% decrease in the volume of the unit cell. The unit-cell parameters of the two isostructures correspond directly with one another. The a and b axes of the ethyl analogue (determined at room temperature) are 6.1% and 6.5% shorter than those of the title compound. Simultaneously, the c axis of the ethyl analogue is 1.5% longer and the β angle is enlarged by 1.0°.

5. Synthesis and crystallization

A glass slide with a sample of 5-propylbarbituric acid embedded in paraffin oil was placed on a hot bench. The sample was melted and left to crystallize. Within a few days, the original crystals had partially converted and cube-shaped single crystals of the title compound had formed.

6. Refinement

Crystal data, data collection and structure refinement details are summarised in Table 2. The data collection was carried out in the manner described by Coles & Gale (2012 ). All H atoms were identified in difference maps. Methyl H atoms were idealized and included as rigid groups allowed to rotate but not tip (C—H = 0.98 Å). H atoms bonded to secondary CH₂ carbon atoms were positioned geometrically (C—H = 0.99 Å). Hydrogen atoms bonded to N atoms were refined with restrained distances [N—H = 0.86 (1) Å]. The hydrogen atom of the hydroxy group was refined freely and the U_iso parameters of all hydrogen atoms were also refined freely.

Table 2
Experimental details

Crystal data
Chemical formula	C₇H₁₀N₂O₄
M_r	186.17
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	100
a, b, c (Å)	10.7862 (8), 6.7093 (5), 11.7365 (6)
β (°)	98.632 (6)
V (Å³)	839.72 (10)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.12
Crystal size (mm)	0.05 × 0.05 × 0.05

Data collection
Diffractometer	Rigaku Saturn724+
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2014 )
T_min, T_max	0.809, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	5354, 1724, 1354
R_int	0.034
(sin θ/λ)_max (Å⁻¹)	0.625

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.095, 1.05
No. of reflections	1724
No. of parameters	138
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.29, −0.20
Computer programs: CrystalClear-SM Expert (Rigaku, 2012 ), CrysAlis PRO (Agilent, 2014), SHELXT (Sheldrick, 2015a ), SHELXL2014/6 (Sheldrick, 2015b ), XP in SHELXTL (Sheldrick, 2008 8) and Mercury (Macrae et al., 2006 ) and publCIF (Westrip, 2010 ).

7. Analysis of structural features

The topology of the HBS was determined and classified with the programs ADS and IsoTest of the TOPOS package (Blatov, 2006 ) in the manner described by Baburin & Blatov (2007 ). The topology graph for the HBS (Fig. 3) is based on a net drawn with the IsoCryst program of the TOPOS package. The HBS of the title structure was defined by the three interactions N—H⋯O(carbonyl), N—H⋯O(hydroxy) and O—H⋯O(carbonyl) listed in Table 1. The molecular packing in the title compound and its ethyl analogue were compared using the program XPac (Gelbrich & Hursthouse, 2005 ). The underlying calculations were based on a comparison of sets of intermolecular geometrical parameters generated from all non-H atomic positions of the title compound, except for the methyl carbon atom, and all 12 non-H atomic positions of the ethyl analogue. A match of two complete clusters consisting of a central molecule and 17 coordinating molecules was obtained with a dissimilarity index (Gelbrich et al., 2012 ) of 5.4, indicating isostructurality of the two compounds with a high degree of packing similarity.

Supporting information

CCDC reference: 1429681

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2056989015018769/zs2347sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989015018769/zs2347Isup2.hkl

checkCIF report

Computing details top

Data collection: CrystalClear-SM Expert (Rigaku, 2012); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014/6 (Sheldrick, 2015b); molecular graphics: XP in SHELXTL (Sheldrick, 20088) and Mercury (Macrae et al., 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

5-Hydroxy-5-propylpyrimidine-2,4,6(1H,3H),5H)-trione top

Crystal data top

C₇H₁₀N₂O₄	F(000) = 392
M_r = 186.17	D_x = 1.473 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 10.7862 (8) Å	Cell parameters from 3013 reflections
b = 6.7093 (5) Å	θ = 2.4–27.5°
c = 11.7365 (6) Å	µ = 0.12 mm⁻¹
β = 98.632 (6)°	T = 100 K
V = 839.72 (10) Å³	Cube, colourless
Z = 4	0.05 × 0.05 × 0.05 mm

Data collection top

Rigaku Saturn724+ diffractometer	1724 independent reflections
Radiation source: Sealed Tube	1354 reflections with I > 2σ(I)
Graphite Monochromator monochromator	R_int = 0.034
Detector resolution: 28.5714 pixels mm^-1	θ_max = 26.4°, θ_min = 2.4°
profile data from ω–scans	h = −12→13
Absorption correction: multi-scan (CrysAlisPro; Agilent, 2014)	k = −8→8
T_min = 0.809, T_max = 1.000	l = −14→14
5354 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)] = 0.037	Hydrogen site location: mixed
wR(F²) = 0.095	H atoms treated by a mixture of independent and constrained refinement
S = 1.05	w = 1/[σ²(F_o²) + (0.0498P)² + 0.1441P] where P = (F_o² + 2F_c²)/3
1724 reflections	(Δ/σ)_max < 0.001
138 parameters	Δρ_max = 0.29 e Å⁻³
2 restraints	Δρ_min = −0.20 e Å⁻³

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
N1	0.75066 (12)	0.60615 (19)	0.37252 (9)	0.0154 (3)
H1	0.8189 (12)	0.536 (3)	0.3792 (16)	0.033 (5)*
O2	0.78456 (10)	0.66277 (16)	0.56534 (8)	0.0201 (3)
C2	0.72112 (13)	0.6895 (2)	0.47207 (11)	0.0147 (3)
N3	0.61584 (11)	0.80699 (19)	0.46014 (9)	0.0150 (3)
H3	0.5995 (14)	0.870 (2)	0.5200 (10)	0.020 (4)*
O4	0.47047 (9)	0.99725 (16)	0.35153 (8)	0.0180 (3)
C4	0.54700 (13)	0.8640 (2)	0.35743 (11)	0.0139 (3)
C5	0.56139 (13)	0.7360 (2)	0.25307 (11)	0.0140 (3)
O6	0.73523 (10)	0.58567 (18)	0.17883 (8)	0.0220 (3)
C6	0.68995 (13)	0.6406 (2)	0.26184 (11)	0.0153 (3)
O7	0.54144 (10)	0.85117 (16)	0.15172 (8)	0.0161 (3)
H7	0.465 (2)	0.864 (3)	0.1270 (16)	0.040 (6)*
C8	0.46287 (14)	0.5674 (2)	0.25253 (11)	0.0158 (3)
H8A	0.4849	0.4858	0.3229	0.021 (4)*
H8B	0.3799	0.6284	0.2557	0.016 (4)*
C9	0.45248 (15)	0.4312 (2)	0.14778 (13)	0.0225 (4)
H9A	0.4526	0.5128	0.0775	0.035 (5)*
H9B	0.5262	0.3417	0.1553	0.033 (5)*
C10	0.33380 (15)	0.3070 (3)	0.13545 (13)	0.0247 (4)
H10A	0.3383	0.2139	0.2003	0.034 (5)*
H10B	0.3253	0.2319	0.0631	0.036 (5)*
H10C	0.2611	0.3948	0.1350	0.044 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0131 (7)	0.0172 (7)	0.0154 (6)	0.0033 (6)	0.0002 (5)	−0.0013 (5)
O2	0.0199 (6)	0.0225 (6)	0.0159 (5)	0.0037 (5)	−0.0043 (4)	−0.0010 (4)
C2	0.0132 (8)	0.0136 (8)	0.0168 (7)	−0.0009 (6)	0.0004 (5)	0.0002 (5)
N3	0.0160 (7)	0.0173 (7)	0.0114 (6)	0.0039 (5)	0.0011 (5)	−0.0022 (5)
O4	0.0170 (6)	0.0205 (6)	0.0161 (5)	0.0058 (5)	0.0005 (4)	−0.0001 (4)
C4	0.0110 (8)	0.0155 (8)	0.0151 (7)	−0.0018 (6)	0.0016 (5)	0.0005 (5)
C5	0.0127 (8)	0.0169 (8)	0.0117 (6)	0.0010 (6)	−0.0003 (5)	0.0009 (5)
O6	0.0173 (6)	0.0323 (7)	0.0168 (5)	0.0046 (5)	0.0042 (4)	−0.0025 (5)
C6	0.0143 (8)	0.0161 (8)	0.0152 (7)	−0.0040 (6)	0.0009 (5)	−0.0003 (5)
O7	0.0143 (6)	0.0202 (6)	0.0128 (5)	−0.0006 (5)	−0.0009 (4)	0.0031 (4)
C8	0.0134 (8)	0.0178 (8)	0.0161 (6)	−0.0004 (6)	0.0021 (5)	0.0014 (6)
C9	0.0226 (9)	0.0200 (9)	0.0256 (8)	−0.0019 (7)	0.0061 (6)	−0.0065 (7)
C10	0.0262 (10)	0.0202 (9)	0.0264 (8)	−0.0030 (7)	−0.0002 (6)	0.0003 (7)

Geometric parameters (Å, º) top

N1—C2	1.3754 (18)	O6—C6	1.2110 (17)
N1—C6	1.3836 (16)	O7—H7	0.84 (2)
N1—H1	0.866 (9)	C8—C9	1.5226 (19)
O2—C2	1.2141 (16)	C8—H8A	0.9900
C2—N3	1.3720 (19)	C8—H8B	0.9900
N3—C4	1.3719 (17)	C9—C10	1.516 (2)
N3—H3	0.860 (9)	C9—H9A	0.9900
O4—C4	1.2117 (17)	C9—H9B	0.9900
C4—C5	1.5228 (19)	C10—H10A	0.9800
C5—O7	1.4076 (16)	C10—H10B	0.9800
C5—C6	1.517 (2)	C10—H10C	0.9800
C5—C8	1.551 (2)

C2—N1—C6	126.31 (13)	N1—C6—C5	115.68 (12)
C2—N1—H1	116.4 (12)	C5—O7—H7	111.6 (14)
C6—N1—H1	116.8 (12)	C9—C8—C5	114.10 (12)
O2—C2—N3	121.52 (13)	C9—C8—H8A	108.7
O2—C2—N1	122.33 (14)	C5—C8—H8A	108.7
N3—C2—N1	116.15 (11)	C9—C8—H8B	108.7
C2—N3—C4	125.47 (12)	C5—C8—H8B	108.7
C2—N3—H3	117.8 (10)	H8A—C8—H8B	107.6
C4—N3—H3	115.6 (11)	C10—C9—C8	111.45 (13)
O4—C4—N3	122.02 (12)	C10—C9—H9A	109.3
O4—C4—C5	121.39 (11)	C8—C9—H9A	109.3
N3—C4—C5	116.26 (13)	C10—C9—H9B	109.3
O7—C5—C6	108.13 (11)	C8—C9—H9B	109.3
O7—C5—C4	110.43 (12)	H9A—C9—H9B	108.0
C6—C5—C4	112.70 (11)	C9—C10—H10A	109.5
O7—C5—C8	112.27 (11)	C9—C10—H10B	109.5
C6—C5—C8	108.15 (12)	H10A—C10—H10B	109.5
C4—C5—C8	105.19 (11)	C9—C10—H10C	109.5
O6—C6—N1	120.87 (14)	H10A—C10—H10C	109.5
O6—C6—C5	123.30 (12)	H10B—C10—H10C	109.5

C6—N1—C2—O2	−174.59 (14)	C2—N1—C6—C5	−16.4 (2)
C6—N1—C2—N3	4.9 (2)	O7—C5—C6—O6	−34.5 (2)
O2—C2—N3—C4	172.08 (14)	C4—C5—C6—O6	−156.87 (14)
N1—C2—N3—C4	−7.4 (2)	C8—C5—C6—O6	87.29 (17)
C2—N3—C4—O4	−165.40 (14)	O7—C5—C6—N1	149.92 (12)
C2—N3—C4—C5	21.1 (2)	C4—C5—C6—N1	27.56 (18)
O4—C4—C5—O7	35.46 (19)	C8—C5—C6—N1	−88.28 (15)
N3—C4—C5—O7	−151.01 (12)	O7—C5—C8—C9	54.47 (16)
O4—C4—C5—C6	156.51 (14)	C6—C5—C8—C9	−64.75 (14)
N3—C4—C5—C6	−29.96 (18)	C4—C5—C8—C9	174.60 (12)
O4—C4—C5—C8	−85.88 (16)	C5—C8—C9—C10	−164.80 (13)
N3—C4—C5—C8	87.64 (14)	C2—C5—C8—C9	−125.69 (11)
C2—N1—C6—O6	167.92 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O7ⁱ	0.87 (1)	2.03 (1)	2.8683 (17)	164 (2)
N3—H3···O4ⁱⁱ	0.86 (1)	2.00 (1)	2.8451 (16)	170 (2)
O7—H7···O2ⁱⁱⁱ	0.84 (2)	1.98 (2)	2.8055 (15)	169 (2)

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

Acknowledgements

We thank Professor Simon Coles (Southampton) for access to the diffractometer used in this study.

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