supplementary materials


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Acta Cryst. (2013). E69, o1235    [ doi:10.1107/S1600536813018175 ]

2-Amino-4,6-dimethylpyrimidine-sorbic acid (1/1)

S. Gomathi and P. T. Muthiah

Abstract top

In the crystal of the title compound, C6H9N3·C6H8O2, the 2-amino-4,6-dimethylpyrimidine and sorbic acid molecules are linked through N-H...O and O-H...N hydrogen bonds, which generate a cyclic bimolecular heterosynthon with an R22(8) graph-set motif. Further, two inversion-related pyrimidine molecules are base-paired via a pair of N-H...N hydrogen bonds, forming a cyclic bimolecular homosynthon with a graph-set of R22(8). A discrete hetero tetrameric supramolecular unit along the b axis is formed by the fusion of two heterosynthons and one homosynthon. An aromatic [pi]-[pi] interaction [centroid-centroid distance = 3.7945 (16) Å] is observed between these tetrameric units.

Comment top

The non-covalent interactions of aminopyrimidine with carboxylic acid derivatives are of immense significance, since they involve in many molecular recognition process of biological functions and protein-drug binding (Hunt et al.,1980). Sorbic acid is an antibacterial agent and widely used as a preservatives. Several salts and co-crystals involving 2-amino-4,6-dimethoxy/dimethyl pyrimidine and various carboxylates (Ebenezer & Muthiah, 2010) have already been reported from our laboratory.

The current investigation focuses on the supramolecular hydrogen-bonded patterns exhibited by the (1:1) co-crystal of 2-amino-4,6-dimethylpyrimidine with sorbic acid. The asymmetric unit of the titled co-crystal consists of one molecule of 2-amino-4,6-dimethylpyrimidine (AMPY) and a molecule of sorbic acid (SA) (Fig. 1). The SA molecule exists in the EE configuration. The extended conformation of SA can be inferred from the four torsion angles, C9—C10—C11—C12 = -178.1 (3)°, C10—C11—C12—C13 = 175.5 (3)°, C11—C12—C13—C14 = -179.0 (3)° and O1—C9—C10—C11 = 168.8 (3)°. The values are in close agreement with those in the literature (Thanigaimani et al., 2007).

The primary supramolecular synthon is assembled via N—H···O and O—H···N hydrogen bonds between the carboxylic group of SA and the amino pyrimidine moiety of AMPY to form a cyclic bimolecular heterosynthon with an R22(8) graph-set motif (Etter, 1990; Bernstein et al., 1995). Two centrosymmetric AMPY molecules are self-assembled to form complementary base pairing via a pair of N—H···N hydrogen bonds to form another R22(8) ring motif. The complementary base pairing involves 2-amino group and ring N3i atom of inversion related pyrimidine moiety of AMPY. The primary and secondary interactions lead to the generation of a discrete and stable linear hetero tetramer along the b axis (Ebenezer & Muthiah, 2012) which is a four-component supramolecule formed by the fusion of two centrosymmetric bimolecular heterosynthons [R22(8)] and a homosynthon [R22(8)] (Fig. 2). These discrete linear hetero tetrameric units are arranged in two dimensional space as sheets without any neighbouring interactions in the same plane.

The pyrimidine moiety of inversion related linear heterotetrameric units present in the parallel planes are stacked by an aromatic ππ interaction in a head to tail fashion (Fig. 3) with the interplanar distance of 3.580 Å, centroid to centroid distance of 3.7945 (16) Å [CgCgi; symmetry code: (i) 1 - x,1 - y,1 - z] and the slip angle of 19.36°.

Related literature top

For aminopyrimidine–carboxylic acid interactions, see: Hunt et al. (1980). For related structures, see: Thanigaimani et al. (2007); Ebenezer & Muthiah (2010, 2012). For hydrogen-bond motifs, see: Bernstein et al. (1995); Etter (1990).

Experimental top

Hot aqueous solutions of 2-amino-4, 6-dimethylpyrimidine (31 mg, Aldrich) and sorbic acid (28 mg, Sisco) were mixed in a 1:1 molar ratio. The resulting solution was warmed over a water bath for half an hour and then kept at room temperature for crystallization. After a week, colorless prismatic crystals were obtained.

Refinement top

The hydrogen atoms for NH2 and OH groups were located in a difference Fourier map and refined freely. All other hydrogen atoms were positioned geometrically (C—H = 0.93–0.96 Å) and were refined using a riding model, with Uiso(H) = 1.2Ueq(C) for CH or 1.5Ueq(C) for CH3.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009), Mercury (Macrae et al., 2008) and POV-RAY (Cason, 2004); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The asymmetric unit of the title compound, shown in 30% probability displacement ellipsoids.
[Figure 2] Fig. 2. A view of supramolecular sheets formed by linear hetero tetramer. [Symmetry code: (i) -x, 1 - y, 1 - z.]
[Figure 3] Fig. 3. A view of aromatic ππ stacking interaction between two parallel planes. [Symmetry code: (i) 1 - x, 1 - y, 1 - z.]
2-Amino-4,6-dimethylpyrimidine–sorbic acid (1/1) top
Crystal data top
C6H9N3·C6H8O2Z = 2
Mr = 235.29F(000) = 252
Triclinic, P1Dx = 1.194 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.8441 (6) ÅCell parameters from 2280 reflections
b = 9.9413 (8) Åθ = 2.3–25.1°
c = 10.2846 (13) ŵ = 0.08 mm1
α = 112.058 (7)°T = 296 K
β = 98.333 (8)°Prism, colourless
γ = 111.306 (5)°0.12 × 0.11 × 0.09 mm
V = 654.69 (13) Å3
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
2280 independent reflections
Radiation source: fine-focus sealed tube1585 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.048
φ and ω scansθmax = 25.1°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 99
Tmin = 0.990, Tmax = 0.993k = 1111
9667 measured reflectionsl = 1212
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)] = 0.069Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.210H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.1185P)2 + 0.152P]
where P = (Fo2 + 2Fc2)/3
2280 reflections(Δ/σ)max < 0.001
169 parametersΔρmax = 0.27 e Å3
0 restraintsΔρmin = 0.28 e Å3
Crystal data top
C6H9N3·C6H8O2γ = 111.306 (5)°
Mr = 235.29V = 654.69 (13) Å3
Triclinic, P1Z = 2
a = 7.8441 (6) ÅMo Kα radiation
b = 9.9413 (8) ŵ = 0.08 mm1
c = 10.2846 (13) ÅT = 296 K
α = 112.058 (7)°0.12 × 0.11 × 0.09 mm
β = 98.333 (8)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
2280 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
1585 reflections with I > 2σ(I)
Tmin = 0.990, Tmax = 0.993Rint = 0.048
9667 measured reflectionsθmax = 25.1°
Refinement top
R[F2 > 2σ(F2)] = 0.069H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.210Δρmax = 0.27 e Å3
S = 1.03Δρmin = 0.28 e Å3
2280 reflectionsAbsolute structure: ?
169 parametersAbsolute structure parameter: ?
0 restraintsRogers parameter: ?
Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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
N10.2301 (3)0.2463 (2)0.49425 (19)0.0543 (7)
N20.0413 (4)0.3650 (3)0.5821 (3)0.0802 (10)
N30.1624 (3)0.4209 (2)0.40922 (19)0.0554 (7)
C20.1464 (3)0.3438 (3)0.4937 (2)0.0539 (7)
C40.2658 (3)0.3961 (3)0.3191 (2)0.0567 (8)
C50.3524 (4)0.2964 (3)0.3122 (3)0.0652 (9)
C60.3326 (3)0.2233 (3)0.4030 (2)0.0582 (8)
C70.2823 (4)0.4809 (4)0.2244 (3)0.0739 (10)
C80.4239 (5)0.1142 (4)0.4044 (3)0.0839 (11)
O10.0710 (4)0.2287 (3)0.7892 (2)0.1067 (10)
O20.2211 (3)0.1013 (2)0.6675 (2)0.0774 (8)
C90.1482 (4)0.1403 (3)0.7730 (3)0.0673 (9)
C100.1635 (4)0.0674 (3)0.8719 (3)0.0765 (10)
C110.2168 (3)0.0479 (3)0.8489 (3)0.0625 (8)
C120.2269 (4)0.1235 (3)0.9435 (3)0.0713 (9)
C130.2681 (4)0.2440 (4)0.9157 (3)0.0788 (11)
C140.2767 (5)0.3265 (4)1.0101 (4)0.0994 (14)
H2A0.017 (4)0.428 (3)0.589 (3)0.072 (7)*
H2B0.036 (4)0.321 (4)0.640 (4)0.095 (10)*
H50.422700.278900.247600.0780*
H7A0.175800.413400.133100.1110*
H7B0.401800.500700.203300.1110*
H7C0.279900.582800.276200.1110*
H8A0.496500.149800.504600.1250*
H8B0.508800.119200.346000.1250*
H8C0.324600.004100.363400.1250*
H20.212 (5)0.160 (4)0.610 (4)0.125 (12)*
H100.132700.106200.958000.0920*
H110.251300.084200.764200.0750*
H120.201600.082001.031800.0860*
H130.295200.283500.827800.0940*
H14A0.209000.301301.079100.1480*
H14B0.409400.288801.063500.1480*
H14C0.217300.442300.948100.1480*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0710 (12)0.0621 (12)0.0571 (10)0.0416 (10)0.0276 (9)0.0408 (9)
N20.129 (2)0.1113 (19)0.0869 (15)0.0945 (18)0.0700 (15)0.0785 (15)
N30.0718 (12)0.0614 (12)0.0544 (10)0.0374 (10)0.0231 (9)0.0399 (9)
C20.0704 (14)0.0616 (13)0.0540 (11)0.0398 (12)0.0244 (10)0.0395 (10)
C40.0640 (13)0.0602 (14)0.0558 (12)0.0265 (12)0.0198 (10)0.0382 (11)
C50.0774 (16)0.0819 (17)0.0676 (14)0.0467 (14)0.0384 (12)0.0496 (13)
C60.0665 (14)0.0676 (15)0.0602 (13)0.0393 (12)0.0246 (11)0.0387 (11)
C70.0909 (18)0.0837 (18)0.0752 (16)0.0404 (15)0.0363 (14)0.0601 (15)
C80.109 (2)0.106 (2)0.0947 (19)0.0792 (19)0.0544 (17)0.0657 (18)
O10.191 (2)0.1244 (18)0.1037 (15)0.1172 (19)0.0929 (16)0.0885 (14)
O20.1068 (14)0.1015 (14)0.0864 (12)0.0691 (12)0.0541 (11)0.0747 (11)
C90.0954 (18)0.0668 (15)0.0625 (14)0.0436 (15)0.0318 (13)0.0433 (12)
C100.119 (2)0.0733 (17)0.0605 (14)0.0492 (17)0.0374 (14)0.0455 (13)
C110.0651 (14)0.0676 (15)0.0638 (13)0.0235 (12)0.0200 (11)0.0460 (12)
C120.0867 (18)0.0665 (16)0.0652 (14)0.0271 (14)0.0169 (12)0.0453 (13)
C130.0751 (17)0.092 (2)0.102 (2)0.0383 (16)0.0352 (15)0.0739 (18)
C140.099 (2)0.093 (2)0.128 (3)0.0343 (18)0.0218 (19)0.087 (2)
Geometric parameters (Å, º) top
O1—C91.214 (5)C7—H7A0.9600
O2—C91.296 (4)C8—H8C0.9600
O2—H20.99 (4)C8—H8A0.9600
N1—C21.355 (4)C8—H8B0.9600
N1—C61.331 (3)C9—C101.468 (4)
N2—C21.323 (4)C10—C111.311 (4)
N3—C41.330 (3)C11—C121.445 (4)
N3—C21.349 (3)C12—C131.293 (5)
N2—H2A0.89 (3)C13—C141.496 (5)
N2—H2B0.86 (4)C10—H100.9300
C4—C71.500 (4)C11—H110.9300
C4—C51.378 (4)C12—H120.9300
C5—C61.376 (4)C13—H130.9300
C6—C81.504 (5)C14—H14A0.9600
C5—H50.9300C14—H14B0.9600
C7—H7C0.9600C14—H14C0.9600
C7—H7B0.9600
O1···N22.946 (4)H2···C82.88 (4)
O2···N12.674 (3)H2···C62.64 (4)
O2···C83.351 (4)H2A···N3iv2.19 (3)
O1···H14Ai2.9100H2A···C4iv3.09 (3)
O1···H2B2.10 (4)H2B···C92.92 (4)
O1···H14Cii2.7200H2B···O12.10 (4)
O1···H8Ciii2.8400H2B···H22.43 (6)
O2···H112.4600H5···H7B2.4700
N1···O22.674 (3)H5···H8B2.4100
N2···N3iv3.076 (4)H5···H13viii2.4400
N2···O12.946 (4)H7B···H52.4700
N3···N2iv3.076 (4)H7C···H8Aix2.4900
N1···H21.70 (4)H8A···H7Cix2.4900
N2···H22.89 (4)H8B···H52.4100
N3···H2Aiv2.19 (3)H8B···H11viii2.4000
C2···C11iii3.521 (3)H8C···O1iii2.8400
C7···C14v3.425 (5)H10···H122.4600
C8···O23.351 (4)H10···H12i2.5700
C11···C2iii3.521 (3)H11···O22.4600
C14···C7vi3.425 (5)H11···H132.4200
C2···H22.68 (4)H11···H8Bviii2.4000
C4···H2Aiv3.09 (3)H12···H102.4600
C6···H22.64 (4)H12···H14A2.4200
C8···H22.88 (4)H12···H10i2.5700
C9···H2B2.92 (4)H13···H112.4200
C10···H14Bvii3.0700H13···H5viii2.4400
H2···N22.89 (4)H14A···H122.4200
H2···C22.68 (4)H14A···O1i2.9100
H2···N11.70 (4)H14B···C10vii3.0700
H2···H2B2.43 (6)H14C···O1x2.7200
C9—O2—H2110 (2)C6—C8—H8A109.00
C2—N1—C6117.4 (2)H8A—C8—H8C110.00
C2—N3—C4116.8 (2)H8B—C8—H8C109.00
C2—N2—H2B118 (2)H8A—C8—H8B109.00
H2A—N2—H2B119 (3)O1—C9—C10121.9 (3)
C2—N2—H2A123.3 (19)O2—C9—C10114.8 (3)
N1—C2—N2117.8 (2)O1—C9—O2123.3 (3)
N2—C2—N3117.5 (3)C9—C10—C11125.5 (3)
N1—C2—N3124.7 (2)C10—C11—C12125.8 (3)
C5—C4—C7121.6 (2)C11—C12—C13125.5 (3)
N3—C4—C7116.8 (2)C12—C13—C14126.8 (3)
N3—C4—C5121.7 (2)C9—C10—H10117.00
C4—C5—C6118.6 (3)C11—C10—H10117.00
N1—C6—C8116.8 (2)C10—C11—H11117.00
C5—C6—C8122.3 (3)C12—C11—H11117.00
N1—C6—C5120.9 (3)C11—C12—H12117.00
C6—C5—H5121.00C13—C12—H12117.00
C4—C5—H5121.00C12—C13—H13117.00
C4—C7—H7A109.00C14—C13—H13117.00
C4—C7—H7C109.00C13—C14—H14A109.00
H7A—C7—H7B109.00C13—C14—H14B109.00
C4—C7—H7B109.00C13—C14—H14C109.00
H7B—C7—H7C109.00H14A—C14—H14B110.00
H7A—C7—H7C110.00H14A—C14—H14C110.00
C6—C8—H8B109.00H14B—C14—H14C109.00
C6—C8—H8C109.00
C6—N1—C2—N2178.8 (2)C7—C4—C5—C6179.5 (3)
C6—N1—C2—N31.1 (3)C4—C5—C6—N10.9 (4)
C2—N1—C6—C50.1 (3)C4—C5—C6—C8179.3 (3)
C2—N1—C6—C8179.7 (2)O1—C9—C10—C11168.8 (3)
C4—N3—C2—N11.1 (3)O2—C9—C10—C1110.4 (5)
C4—N3—C2—N2178.9 (2)C9—C10—C11—C12178.1 (3)
C2—N3—C4—C50.0 (3)C10—C11—C12—C13175.5 (3)
C2—N3—C4—C7179.6 (2)C11—C12—C13—C14179.0 (3)
N3—C4—C5—C61.0 (4)
Symmetry codes: (i) x, y, z+2; (ii) x, y+1, z; (iii) x, y, z+1; (iv) x, y+1, z+1; (v) x, y+1, z1; (vi) x, y1, z+1; (vii) x+1, y, z+2; (viii) x+1, y, z+1; (ix) x+1, y+1, z+1; (x) x, y1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···N10.99 (4)1.70 (4)2.674 (3)167 (4)
N2—H2A···N3iv0.89 (3)2.19 (3)3.076 (4)176 (2)
N2—H2B···O10.86 (4)2.10 (4)2.946 (4)171 (3)
Symmetry code: (iv) x, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC6H9N3·C6H8O2
Mr235.29
Crystal system, space groupTriclinic, P1
Temperature (K)296
a, b, c (Å)7.8441 (6), 9.9413 (8), 10.2846 (13)
α, β, γ (°)112.058 (7), 98.333 (8), 111.306 (5)
V3)654.69 (13)
Z2
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.12 × 0.11 × 0.09
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2008)
Tmin, Tmax0.990, 0.993
No. of measured, independent and
observed [I > 2σ(I)] reflections
9667, 2280, 1585
Rint0.048
(sin θ/λ)max1)0.596
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.069, 0.210, 1.03
No. of reflections2280
No. of parameters169
No. of restraints0
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.27, 0.28

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009), Mercury (Macrae et al., 2008) and POV-RAY (Cason, 2004), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2···N10.99 (4)1.70 (4)2.674 (3)167 (4)
N2—H2A···N3i0.89 (3)2.19 (3)3.076 (4)176 (2)
N2—H2B···O10.86 (4)2.10 (4)2.946 (4)171 (3)
Symmetry code: (i) x, y+1, z+1.
Acknowledgements top

SG thanks the UGC–SAP, India, for the award of an RFSMS. The authors thank the DST India (FIST programme) for the use of Bruker SMART APEXII diffractometer at the School of Chemistry, Bharathidasan University, Tiruchirappalli, Tamilnadu, India.

references
References top

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Ebenezer, S. & Muthiah, P. T. (2010). Acta Cryst. E66, o2634–o2635.

Ebenezer, S. & Muthiah, P. T. (2012). Cryst. Growth Des. 12, 3766–3785.

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Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.

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Spek, A. L. (2009). Acta Cryst. D65, 148–155.

Thanigaimani, K., Muthiah, P. T. & Lynch, D. E. (2007). Acta Cryst. E63, o4450–o4451.