Pyrimidine-2,4-diamine acetone monosolvate

Draguta, S.; Sandhu, B.; Khrustalev, V.N.; Fonari, M.S.; Timofeeva, T.V.

doi:10.1107/S1600536813001025

organic compounds

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Volume 69| Part 2| February 2013| Page o251

doi:10.1107/S1600536813001025

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Pyrimidine-2,4-diamine acetone monosolvate

Sergiu Draguta,^a ^* Bhupinder Sandhu,^b Victor N. Khrustalev,^c Marina S. Fonari ^d and Tatiana V. Timofeeva ^b

^aD. Ghitu Institute of Electronic Engineering and Nanotechnologies, 3/3 Academy Street, MD-2028, Chisinau, Republic of Moldova, ^bDepartment of Biology & Chemistry, New Mexico Highlands University, 803 University Avenue, Las Vegas, NM 87701, USA, ^cX-Ray Structural Centre, A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Street, B-334, Moscow 119991, Russian Federation, and ^dInstitute of Applied Physics Academy of Science of Moldova, 5 Academy Street, MD-2028, Chisinau, Republic of Moldova.
^*Correspondence e-mail: sergiudraguta@gmail.com

(Received 1 January 2013; accepted 11 January 2013; online 19 January 2013)

In the title compound, C₄H₆N₄·C₃H₆O, the pyrimidine-2,4-diamine molecule is nearly planar (r.m.s. deviation = 0.005 Å), with the endocyclic angles covering the range 114.36 (10)–126.31 (10)°. In the crystal, N—H⋯N and N—H⋯O hydrogen bonds link the molecules into ribbons along [101], and weak C—H⋯π interactions consolidate further the crystal packing.

Related literature

For the biological activity of pyrimidine derivatives, see: Hall et al. (1993 ); Gengeliczki et al. (2011 ). For the crystal structures of related compounds, see: Bertolasi et al. (2002 ); Draguta et al. (2012 ). For bond lengths in organic compounds, see: Allen et al. (1987 ). For hydrogen-bonding graph-set notation, see: Bernstein et al. (1995 ).

Experimental

Crystal data

C₄H₆N₄·C₃H₆O
M_r = 168.21
Monoclinic, P 2₁ /c
a = 8.1594 (15) Å
b = 12.728 (2) Å
c = 8.7663 (16) Å
β = 99.395 (3)°
V = 898.2 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 296 K
0.30 × 0.25 × 0.20 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ) T_min = 0.974, T_max = 0.982
9693 measured reflections
2170 independent reflections
1752 reflections with I > 2σ(I)
R_int = 0.051

Refinement

R[F² > 2σ(F²)] = 0.048
wR(F²) = 0.139
S = 1.07
2170 reflections
127 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.28 e Å⁻³
Δρ_min = −0.28 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the pyrimidine ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯N1ⁱ	0.875 (18)	2.191 (18)	3.0608 (18)	177.3 (15)
N2—H2B⋯O1	0.871 (16)	2.247 (19)	3.0990 (17)	164.7 (16)
N4—H4A⋯O1ⁱⁱ	0.879 (17)	2.170 (18)	2.9141 (16)	142.2 (15)
N4—H4B⋯N3ⁱⁱ	0.900 (18)	2.120 (19)	3.0171 (17)	174.9 (15)
C9—H9C⋯Cgⁱⁱⁱ	0.96	2.63	3.5484 (17)	159
Symmetry codes: (i) -x, -y+1, -z; (ii) -x+1, -y+1, -z+1; (iii) $[-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2005 ); cell refinement: SAINT (Bruker, 2001 ); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536813001025/cv5381sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813001025/cv5381Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813001025/cv5381Isup3.cml

checkCIF report

Comment top

Pyrimidine derivatives are biologically important compounds, because they occur in nature as components of nucleic acids. Pyrimidine-2,4-diamine reacts with 3,4,5-trimethoxybenzyl to form trimethoprim which acts as the nucleic acid inhibitor (Hall et al., 1993) as well as with 3,7-dimethylxanthine to form clusters which represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine (Gengeliczki et al. 2011). In the area of drug design and pharmacore mapping, there are several compounds comprising the 2,4-diaminopyrimidinium cations and β- or ζ-diketoenolate anions bound into supramolecular synthons by intermolecular hydrogen bonds (Bertolasi et al., 2002). The presented here crystal structure of the title compound, C₄H₆N₄.C₃H₆O, (I) (Figure 1) was determined to study its hydrogen bonding system and to use it in the future for the design of co-crystals with particular properties.

The asymmetric unit of I consists of a pyrimidine-2,4-diamine molecule and an acetone solvate molecule. The pyrimidine-2,4-diamine molecule is planar (r.m.s. = 0.005 Å), with the endocyclic angles covering range of 114.36 (10)–126.31 (10)°. The endocyclic angles at the C2, C4 and C6 carbon atoms adjacent to the N1 and N3 heteroatoms are larger than 120°, and those at the other atoms of the ring are smaller than 120°. The analogous distribution of the endocyclic angles was recently observed by us within the related pyridine-2,5-diamine (Draguta et al., 2012). The bond lengths have the usual values (Allen et al., 1987).

In the crystal, each pyrimidine molecule is connected to two others ones by the intermolecular N2—H2A···N1ⁱ and N4—H4B···N3ⁱⁱ hydrogen bonds (centrosymmetric R₂² (8) ring motifs (Bernstein et al., 1995); Table 1), forming the infinite ribbons toward [101] (Figure 2). The acetone molecules are bonded to the ribbons as pendant molecules via two intermolecular N2—H2B···O1 and N4—H4A···O1ⁱⁱ hydrogen bonds (Table 1, Figure 2), and are almost coplanar to the ribbon planes (the dihedral angle between the 2,4-pyrimidine and acetone molecules is 7.33 (2)°). The ribbons are packed into layers parallel to (1 0 1), with the interlayer distance of 3.8827 (16) Å). The layers are linked to each other by the intermolecular C9—H9C···π (pyrimidine ring) interactions (Table 1).

Related literature top

For the biological activity of pyrimidine derivatives, see: Hall et al. (1993); Gengeliczki et al. (2011). For the crystal structures of related compounds, see: Bertolasi et al. (2002); Draguta et al. (2012). For bond lengths in organic compounds, see: Allen et al. (1987). For hydrogen-bonding graph-set notation, see: Bernstein et al. (1995).

Experimental top

The compound I was obtained commercially (Aldrich) as a fine-crystalline powder. Crystals suitable for the X-ray diffraction study were grown by slow evaporation from acetone solution. The crystals of I are very sensitive to air and moisture. Therefore, to keep the quality of the crystal during the experiment, the crystal of I was mounted in vaseline oil.

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. Molecular structure of I. Displacement ellipsoids are shown at the 50% probability level. H atoms are presented as small spheres of arbitrary radius.
	Fig. 2. A portion of the crystal packing showing the H-bonded ribbons toward [101]. Dashed lines indicate the intermolecular N—H···N and N—H···O hydrogen bonds.

Pyrimidine-2,4-diamine acetone monosolvate top

Crystal data top

C₄H₆N₄·C₃H₆O	F(000) = 360
M_r = 168.21	D_x = 1.244 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 8851 reflections
a = 8.1594 (15) Å	θ = 2.3–32.1°
b = 12.728 (2) Å	µ = 0.09 mm⁻¹
c = 8.7663 (16) Å	T = 296 K
β = 99.395 (3)°	Prism, colourless
V = 898.2 (3) Å³	0.30 × 0.25 × 0.20 mm
Z = 4

Data collection top

Bruker APEXII CCD diffractometer	2170 independent reflections
Radiation source: fine-focus sealed tube	1752 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.051
ϕ and ω scans	θ_max = 28.0°, θ_min = 2.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −10→10
T_min = 0.974, T_max = 0.982	k = −16→16
9693 measured reflections	l = −11→11

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)] = 0.048	Hydrogen site location: difference Fourier map
wR(F²) = 0.139	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	w = 1/[σ²(F_o²) + (0.0884P)²] where P = (F_o² + 2F_c²)/3
2170 reflections	(Δ/σ)_max < 0.001
127 parameters	Δρ_max = 0.28 e Å⁻³
0 restraints	Δρ_min = −0.28 e Å⁻³

Crystal data top

C₄H₆N₄·C₃H₆O	V = 898.2 (3) Å³
M_r = 168.21	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 8.1594 (15) Å	µ = 0.09 mm⁻¹
b = 12.728 (2) Å	T = 296 K
c = 8.7663 (16) Å	0.30 × 0.25 × 0.20 mm
β = 99.395 (3)°

Data collection top

Bruker APEXII CCD diffractometer	2170 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	1752 reflections with I > 2σ(I)
T_min = 0.974, T_max = 0.982	R_int = 0.051
9693 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.048	0 restraints
wR(F²) = 0.139	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	Δρ_max = 0.28 e Å⁻³
2170 reflections	Δρ_min = −0.28 e Å⁻³
127 parameters

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
N1	0.12301 (13)	0.39554 (8)	0.11848 (12)	0.0224 (3)
C2	0.19664 (15)	0.47490 (9)	0.20658 (14)	0.0191 (3)
N2	0.14277 (14)	0.57309 (9)	0.16744 (13)	0.0255 (3)
H2A	0.0691 (19)	0.5838 (13)	0.0852 (18)	0.025 (4)*
H2B	0.197 (2)	0.6249 (13)	0.2183 (19)	0.033 (4)*
N3	0.31691 (12)	0.46530 (8)	0.33213 (12)	0.0187 (3)
C4	0.36727 (15)	0.36728 (9)	0.37483 (14)	0.0190 (3)
N4	0.48650 (14)	0.35701 (8)	0.49903 (13)	0.0240 (3)
H4A	0.5237 (19)	0.2944 (14)	0.5294 (18)	0.033 (4)*
H4B	0.539 (2)	0.4120 (14)	0.5498 (19)	0.031 (4)*
C5	0.29627 (16)	0.27903 (10)	0.29098 (15)	0.0245 (3)
H5	0.3283	0.2109	0.3202	0.029*
C6	0.17840 (16)	0.29891 (10)	0.16502 (15)	0.0248 (3)
H6	0.1329	0.2417	0.1070	0.030*
O1	0.28515 (12)	0.78374 (7)	0.30884 (11)	0.0285 (3)
C7	0.30086 (19)	0.97014 (11)	0.31631 (19)	0.0333 (4)
H7A	0.3699	0.9583	0.4144	0.050*
H7B	0.2067	1.0120	0.3308	0.050*
H7C	0.3635	1.0063	0.2489	0.050*
C8	0.24238 (15)	0.86704 (9)	0.24592 (14)	0.0223 (3)
C9	0.12660 (17)	0.86932 (11)	0.09351 (16)	0.0297 (3)
H9A	0.1316	0.8032	0.0418	0.045*
H9B	0.1592	0.9246	0.0303	0.045*
H9C	0.0151	0.8816	0.1112	0.045*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0249 (6)	0.0168 (5)	0.0226 (5)	−0.0012 (4)	−0.0046 (4)	−0.0021 (4)
C2	0.0203 (6)	0.0162 (6)	0.0199 (6)	−0.0007 (4)	0.0003 (5)	−0.0009 (4)
N2	0.0304 (6)	0.0153 (6)	0.0260 (6)	−0.0001 (4)	−0.0093 (5)	0.0003 (4)
N3	0.0209 (5)	0.0125 (5)	0.0212 (5)	−0.0003 (4)	−0.0012 (4)	0.0001 (4)
C4	0.0190 (6)	0.0155 (6)	0.0217 (6)	−0.0001 (4)	0.0006 (4)	0.0003 (4)
N4	0.0255 (6)	0.0134 (5)	0.0288 (6)	0.0008 (4)	−0.0080 (4)	0.0012 (4)
C5	0.0270 (7)	0.0138 (6)	0.0303 (7)	0.0007 (5)	−0.0025 (5)	−0.0011 (5)
C6	0.0279 (7)	0.0162 (6)	0.0277 (6)	−0.0012 (5)	−0.0027 (5)	−0.0046 (5)
O1	0.0325 (5)	0.0184 (5)	0.0314 (5)	0.0024 (4)	−0.0042 (4)	0.0037 (4)
C7	0.0376 (8)	0.0210 (7)	0.0424 (8)	−0.0053 (6)	0.0099 (6)	−0.0066 (6)
C8	0.0217 (6)	0.0182 (6)	0.0268 (6)	0.0007 (5)	0.0029 (5)	0.0014 (5)
C9	0.0271 (7)	0.0311 (7)	0.0289 (7)	0.0032 (5)	−0.0017 (5)	0.0059 (5)

Geometric parameters (Å, º) top

N1—C6	1.3503 (16)	C5—H5	0.9300
N1—C2	1.3513 (16)	C6—H6	0.9300
C2—N2	1.3505 (16)	O1—C8	1.2196 (15)
C2—N3	1.3552 (16)	C7—C8	1.4948 (18)
N2—H2A	0.871 (16)	C7—H7A	0.9600
N2—H2B	0.875 (18)	C7—H7B	0.9600
N3—C4	1.3474 (15)	C7—H7C	0.9600
C4—N4	1.3428 (16)	C8—C9	1.5054 (18)
C4—C5	1.4137 (17)	C9—H9A	0.9600
N4—H4A	0.879 (17)	C9—H9B	0.9600
N4—H4B	0.900 (18)	C9—H9C	0.9600
C5—C6	1.3644 (18)

C6—N1—C2	114.36 (11)	N1—C6—H6	117.6
N2—C2—N1	116.78 (11)	C5—C6—H6	117.6
N2—C2—N3	116.88 (11)	C8—C7—H7A	109.5
N1—C2—N3	126.32 (11)	C8—C7—H7B	109.5
C2—N2—H2A	120.5 (11)	H7A—C7—H7B	109.5
C2—N2—H2B	116.9 (11)	C8—C7—H7C	109.5
H2A—N2—H2B	121.8 (15)	H7A—C7—H7C	109.5
C4—N3—C2	117.17 (10)	H7B—C7—H7C	109.5
N4—C4—N3	117.59 (11)	O1—C8—C7	121.87 (12)
N4—C4—C5	121.69 (11)	O1—C8—C9	120.66 (11)
N3—C4—C5	120.71 (11)	C7—C8—C9	117.47 (12)
C4—N4—H4A	120.2 (11)	C8—C9—H9A	109.5
C4—N4—H4B	123.3 (10)	C8—C9—H9B	109.5
H4A—N4—H4B	116.2 (15)	H9A—C9—H9B	109.5
C6—C5—C4	116.64 (12)	C8—C9—H9C	109.5
C6—C5—H5	121.7	H9A—C9—H9C	109.5
C4—C5—H5	121.7	H9B—C9—H9C	109.5
N1—C6—C5	124.78 (11)

C6—N1—C2—N2	−178.34 (11)	C2—N3—C4—C5	−0.04 (18)
C6—N1—C2—N3	0.25 (19)	N4—C4—C5—C6	−178.77 (12)
N2—C2—N3—C4	177.85 (11)	N3—C4—C5—C6	1.21 (19)
N1—C2—N3—C4	−0.75 (19)	C2—N1—C6—C5	1.10 (19)
C2—N3—C4—N4	179.95 (11)	C4—C5—C6—N1	−1.8 (2)

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the pyrimidine ring.

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.875 (18)	2.191 (18)	3.0608 (18)	177.3 (15)
N2—H2B···O1	0.871 (16)	2.247 (19)	3.0990 (17)	164.7 (16)
N4—H4A···O1ⁱⁱ	0.879 (17)	2.170 (18)	2.9141 (16)	142.2 (15)
N4—H4B···N3ⁱⁱ	0.900 (18)	2.120 (19)	3.0171 (17)	174.9 (15)
C9—H9C···Cgⁱⁱⁱ	0.96	2.63	3.5484 (17)	159

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

Experimental details

Crystal data
Chemical formula	C₄H₆N₄·C₃H₆O
M_r	168.21
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	296
a, b, c (Å)	8.1594 (15), 12.728 (2), 8.7663 (16)
β (°)	99.395 (3)
V (Å³)	898.2 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.30 × 0.25 × 0.20

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2003)
T_min, T_max	0.974, 0.982
No. of measured, independent and observed [I > 2σ(I)] reflections	9693, 2170, 1752
R_int	0.051
(sin θ/λ)_max (Å⁻¹)	0.661

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.048, 0.139, 1.07
No. of reflections	2170
No. of parameters	127
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.28, −0.28

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2001), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

Cg is the centroid of the pyrimidine ring.

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.875 (18)	2.191 (18)	3.0608 (18)	177.3 (15)
N2—H2B···O1	0.871 (16)	2.247 (19)	3.0990 (17)	164.7 (16)
N4—H4A···O1ⁱⁱ	0.879 (17)	2.170 (18)	2.9141 (16)	142.2 (15)
N4—H4B···N3ⁱⁱ	0.900 (18)	2.120 (19)	3.0171 (17)	174.9 (15)
C9—H9C···Cgⁱⁱⁱ	0.96	2.63	3.5484 (17)	159

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

Acknowledgements

The authors are grateful for NSF support via DMR grant 0934212 (PREM) and CHE 0832622.

References

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