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ISSN: 2056-9890

Pyrimidine-2,4-di­amine acetone monosolvate

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[Hall, I. A., Campbell, K. L., Chambers, M. D. & Davis, C. N. (1993). J. Am. Vet. Med. Assoc. 202, 1959-1962.]); Gengeliczki et al. (2011[Gengeliczki, Z., Callahan, M. P., Kabeláč, M., Rijs, A. M. & de Vries, M. S. (2011). J. Phys. Chem. A, 115, 11423-11427.]). For the crystal structures of related compounds, see: Bertolasi et al. (2002[Bertolasi, V., Pretto, L., Gilli, P., Ferretti, V. & Gilli, G. (2002). New J. Chem. 26, 1559-1566.]); Draguta et al. (2012[Draguta, S., Khrustalev, V. N., Fonari, M. S., Antipin, M. Y. & Timofeeva, T. V. (2012). Acta Cryst. E68, o3353.]). For bond lengths in organic compounds, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]). For hydrogen-bonding graph-set notation, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C4H6N4·C3H6O

  • Mr = 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[Sheldrick, G. M. (2003). SADABS. University of Göttingen, Germany.]) Tmin = 0.974, Tmax = 0.982

  • 9693 measured reflections

  • 2170 independent reflections

  • 1752 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.28 e Å−3

  • Δρmin = −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 DA 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—H9CCgiii 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[Bruker (2005). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2001[Bruker (2001). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information


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.

Refinement top

The hydrogen atoms of the amino groups were localized in the difference Fourier maps and refined isotropically. The other hydrogen atoms were placed in the calculated positions with C—H = 0.93 Å (CH-groups) and 0.96 Å (CH3-groups) and refined in the riding model with fixed isotropic displacement parameters [Uiso(H) = 1.5Ueq(C) for the CH3-groups and 1.2Ueq(C) for the CH-groups].

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
[Figure 1] 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.
[Figure 2] 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·C3H6OF(000) = 360
Mr = 168.21Dx = 1.244 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 8851 reflections
a = 8.1594 (15) Åθ = 2.3–32.1°
b = 12.728 (2) ŵ = 0.09 mm1
c = 8.7663 (16) ÅT = 296 K
β = 99.395 (3)°Prism, colourless
V = 898.2 (3) Å30.30 × 0.25 × 0.20 mm
Z = 4
Data collection top
Bruker APEXII CCD
diffractometer
2170 independent reflections
Radiation source: fine-focus sealed tube1752 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.051
ϕ and ω scansθmax = 28.0°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 1010
Tmin = 0.974, Tmax = 0.982k = 1616
9693 measured reflectionsl = 1111
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: difference Fourier map
wR(F2) = 0.139H atoms treated by a mixture of independent and constrained refinement
S = 1.07 w = 1/[σ2(Fo2) + (0.0884P)2]
where P = (Fo2 + 2Fc2)/3
2170 reflections(Δ/σ)max < 0.001
127 parametersΔρmax = 0.28 e Å3
0 restraintsΔρmin = 0.28 e Å3
Crystal data top
C4H6N4·C3H6OV = 898.2 (3) Å3
Mr = 168.21Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.1594 (15) ŵ = 0.09 mm1
b = 12.728 (2) ÅT = 296 K
c = 8.7663 (16) Å0.30 × 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)
Tmin = 0.974, Tmax = 0.982Rint = 0.051
9693 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0480 restraints
wR(F2) = 0.139H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.28 e Å3
2170 reflectionsΔρmin = 0.28 e Å3
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
xyzUiso*/Ueq
N10.12301 (13)0.39554 (8)0.11848 (12)0.0224 (3)
C20.19664 (15)0.47490 (9)0.20658 (14)0.0191 (3)
N20.14277 (14)0.57309 (9)0.16744 (13)0.0255 (3)
H2A0.0691 (19)0.5838 (13)0.0852 (18)0.025 (4)*
H2B0.197 (2)0.6249 (13)0.2183 (19)0.033 (4)*
N30.31691 (12)0.46530 (8)0.33213 (12)0.0187 (3)
C40.36727 (15)0.36728 (9)0.37483 (14)0.0190 (3)
N40.48650 (14)0.35701 (8)0.49903 (13)0.0240 (3)
H4A0.5237 (19)0.2944 (14)0.5294 (18)0.033 (4)*
H4B0.539 (2)0.4120 (14)0.5498 (19)0.031 (4)*
C50.29627 (16)0.27903 (10)0.29098 (15)0.0245 (3)
H50.32830.21090.32020.029*
C60.17840 (16)0.29891 (10)0.16502 (15)0.0248 (3)
H60.13290.24170.10700.030*
O10.28515 (12)0.78374 (7)0.30884 (11)0.0285 (3)
C70.30086 (19)0.97014 (11)0.31631 (19)0.0333 (4)
H7A0.36990.95830.41440.050*
H7B0.20671.01200.33080.050*
H7C0.36351.00630.24890.050*
C80.24238 (15)0.86704 (9)0.24592 (14)0.0223 (3)
C90.12660 (17)0.86932 (11)0.09351 (16)0.0297 (3)
H9A0.13160.80320.04180.045*
H9B0.15920.92460.03030.045*
H9C0.01510.88160.11120.045*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0249 (6)0.0168 (5)0.0226 (5)0.0012 (4)0.0046 (4)0.0021 (4)
C20.0203 (6)0.0162 (6)0.0199 (6)0.0007 (4)0.0003 (5)0.0009 (4)
N20.0304 (6)0.0153 (6)0.0260 (6)0.0001 (4)0.0093 (5)0.0003 (4)
N30.0209 (5)0.0125 (5)0.0212 (5)0.0003 (4)0.0012 (4)0.0001 (4)
C40.0190 (6)0.0155 (6)0.0217 (6)0.0001 (4)0.0006 (4)0.0003 (4)
N40.0255 (6)0.0134 (5)0.0288 (6)0.0008 (4)0.0080 (4)0.0012 (4)
C50.0270 (7)0.0138 (6)0.0303 (7)0.0007 (5)0.0025 (5)0.0011 (5)
C60.0279 (7)0.0162 (6)0.0277 (6)0.0012 (5)0.0027 (5)0.0046 (5)
O10.0325 (5)0.0184 (5)0.0314 (5)0.0024 (4)0.0042 (4)0.0037 (4)
C70.0376 (8)0.0210 (7)0.0424 (8)0.0053 (6)0.0099 (6)0.0066 (6)
C80.0217 (6)0.0182 (6)0.0268 (6)0.0007 (5)0.0029 (5)0.0014 (5)
C90.0271 (7)0.0311 (7)0.0289 (7)0.0032 (5)0.0017 (5)0.0059 (5)
Geometric parameters (Å, º) top
N1—C61.3503 (16)C5—H50.9300
N1—C21.3513 (16)C6—H60.9300
C2—N21.3505 (16)O1—C81.2196 (15)
C2—N31.3552 (16)C7—C81.4948 (18)
N2—H2A0.871 (16)C7—H7A0.9600
N2—H2B0.875 (18)C7—H7B0.9600
N3—C41.3474 (15)C7—H7C0.9600
C4—N41.3428 (16)C8—C91.5054 (18)
C4—C51.4137 (17)C9—H9A0.9600
N4—H4A0.879 (17)C9—H9B0.9600
N4—H4B0.900 (18)C9—H9C0.9600
C5—C61.3644 (18)
C6—N1—C2114.36 (11)N1—C6—H6117.6
N2—C2—N1116.78 (11)C5—C6—H6117.6
N2—C2—N3116.88 (11)C8—C7—H7A109.5
N1—C2—N3126.32 (11)C8—C7—H7B109.5
C2—N2—H2A120.5 (11)H7A—C7—H7B109.5
C2—N2—H2B116.9 (11)C8—C7—H7C109.5
H2A—N2—H2B121.8 (15)H7A—C7—H7C109.5
C4—N3—C2117.17 (10)H7B—C7—H7C109.5
N4—C4—N3117.59 (11)O1—C8—C7121.87 (12)
N4—C4—C5121.69 (11)O1—C8—C9120.66 (11)
N3—C4—C5120.71 (11)C7—C8—C9117.47 (12)
C4—N4—H4A120.2 (11)C8—C9—H9A109.5
C4—N4—H4B123.3 (10)C8—C9—H9B109.5
H4A—N4—H4B116.2 (15)H9A—C9—H9B109.5
C6—C5—C4116.64 (12)C8—C9—H9C109.5
C6—C5—H5121.7H9A—C9—H9C109.5
C4—C5—H5121.7H9B—C9—H9C109.5
N1—C6—C5124.78 (11)
C6—N1—C2—N2178.34 (11)C2—N3—C4—C50.04 (18)
C6—N1—C2—N30.25 (19)N4—C4—C5—C6178.77 (12)
N2—C2—N3—C4177.85 (11)N3—C4—C5—C61.21 (19)
N1—C2—N3—C40.75 (19)C2—N1—C6—C51.10 (19)
C2—N3—C4—N4179.95 (11)C4—C5—C6—N11.8 (2)
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the pyrimidine ring.
D—H···AD—HH···AD···AD—H···A
N2—H2A···N1i0.875 (18)2.191 (18)3.0608 (18)177.3 (15)
N2—H2B···O10.871 (16)2.247 (19)3.0990 (17)164.7 (16)
N4—H4A···O1ii0.879 (17)2.170 (18)2.9141 (16)142.2 (15)
N4—H4B···N3ii0.900 (18)2.120 (19)3.0171 (17)174.9 (15)
C9—H9C···Cgiii0.962.633.5484 (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 formulaC4H6N4·C3H6O
Mr168.21
Crystal system, space groupMonoclinic, P21/c
Temperature (K)296
a, b, c (Å)8.1594 (15), 12.728 (2), 8.7663 (16)
β (°) 99.395 (3)
V3)898.2 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.30 × 0.25 × 0.20
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.974, 0.982
No. of measured, independent and
observed [I > 2σ(I)] reflections
9693, 2170, 1752
Rint0.051
(sin θ/λ)max1)0.661
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.048, 0.139, 1.07
No. of reflections2170
No. of parameters127
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N2—H2A···N1i0.875 (18)2.191 (18)3.0608 (18)177.3 (15)
N2—H2B···O10.871 (16)2.247 (19)3.0990 (17)164.7 (16)
N4—H4A···O1ii0.879 (17)2.170 (18)2.9141 (16)142.2 (15)
N4—H4B···N3ii0.900 (18)2.120 (19)3.0171 (17)174.9 (15)
C9—H9C···Cgiii0.962.633.5484 (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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