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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o267–o268.
Published online 2007 December 12. doi:  10.1107/S1600536807065683
PMCID: PMC2915323

N,N′-Bis(pyrimidin-2-yl)terephthalamide dihydrate1

Abstract

The organic mol­ecule of the title compound, C16H12N6O2·2H2O, lies across a crystallographic inversion centre. The dihedral angle between the pyrimidine and benzene rings is 80.78 (6)°. The two pyrimidine rings are parallel by virtue of the centre of symmetry. The pyrimidine and benzene rings form dihedral angles of 41.41 (7) and 40.26 (7)°, respectively, with the amide plane. The mol­ecules are linked by N—H(...)N and C—H(...)N hydrogen bonds into a two-dimensional network parallel to the (1An external file that holds a picture, illustration, etc.
Object name is e-64-0o267-efi1.jpg1) plane. O—H(...)O and C—H(...)O hydrogen bonds involving the water mol­ecules link the adjacent layers into a three-dimensional network. In addition, a C—H(...)π inter­action involving the benzene ring is observed.

Related literature

For bond-length data, see: Allen et al. (1987 [triangle]). For related literature on supra­molecular chemistry, see: Desiraju (1989 [triangle]); Lehn (1995 [triangle]). For related structures, see: Goswami, Jana, Das et al. (2007 [triangle]); Goswami, Jana, Hazra et al. (2007 [triangle]). For related literature on the coordination chemistry and applications of amino­pyrimidine derivatives, see: Aakeroy et al. (2006 [triangle]); Etter (1990 [triangle]); Fun et al. (2006 [triangle]); Gallagher et al. (2004 [triangle]); Goswami & Mahapatra (1999 [triangle]); Smith et al. (1998 [triangle]); Wang et al. (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o267-scheme1.jpg

Experimental

Crystal data

  • C16H12N6O2·2H2O
  • M r = 356.35
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o267-efi2.jpg
  • a = 5.0733 (1) Å
  • b = 8.3233 (1) Å
  • c = 9.9622 (2) Å
  • α = 68.220 (1)°
  • β = 75.441 (1)°
  • γ = 82.333 (1)°
  • V = 377.72 (1) Å3
  • Z = 1
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 100.0 (1) K
  • 0.33 × 0.22 × 0.08 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.963, T max = 0.991
  • 12751 measured reflections
  • 2202 independent reflections
  • 1982 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.044
  • wR(F 2) = 0.106
  • S = 1.12
  • 2202 reflections
  • 154 parameters
  • 3 restraints
  • All H-atom parameters refined
  • Δρmax = 0.39 e Å−3
  • Δρmin = −0.26 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: APEX2; data reduction: SAINT (Bruker, 2005 [triangle]); program(s) used to solve structure: SHELXTL (Sheldrick, 1998 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2003 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536807065683/ci2534sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807065683/ci2534Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

SJ, AH and SG acknowledge the DST (grant No. SR/S1/OC-13/2005) and CSIR [grant No. 01(1913)/04/EMR-II], Government of India, for financial support. SJ and AH thank the CSIR, Government of India, for research fellowships. SC thanks the Prince of Songkla University, Thailand, for support. The authors also thank the Malaysian Government and Universiti Sains Malaysia for a Scientific Advancement Grant Allocation (SAGA, grant No. 304/PFIZIK/653003/A118).

supplementary crystallographic information

Comment

Substituted 2-aminopyrimidines are very important compounds in molecular recognition and supramolecular chemistry (Desiraju, 1989; Lehn, 1995) for the presence of nice donor-acceptor arrays (Aakeroy et al., 2006; Etter, 1990; Fun et al., 2006; Gallagher, et al., 2004; Goswami & Mahapatra, 1999). The donor-acceptor arrangement of the title molecule differs from the 2-aminopyrimidine based compounds (Goswami, Jana, Das et al., 2007; Goswami, Jana, Hazra et al., 2007). These types of compounds are also important for the metal coordination and related studies (Smith et al., 1998; Wang et al., 2006). The coordination chemistry of the title compound is under investigations.

Molecules of the title compound lie across a crystallographic inversion centre (Fig. 1). All bond lengths and angles have normal values (Allen et al., 1987). The N,N-di-pyrimidin-2-yl-terepthalamide molecule has a staggered conformation. The orientation of the pyrimidine ring (C1–C4/N1/N2) with respect to the benzene ring (C6–C8/C6A–C8A) can be described by the dihedral angle formed by these planes of 80.78 (6)° and the torsion angle C4–N3–C5–C6 of -169.50 (11)°. The two pyrimidine rings are parallel by virtue of the centre of symmetry. The pyrimidine and benzene rings form dihedral angles of 41.41 (7)° and 40.26 (7)°, respectively, with the amide plane.

The structure shows O—H···O and C—H···O hydrogen bond between water and N,N-di-pyrimidin-2-yl-terepthalamide molecule. In the crystal packing (Fig. 2), the molecules are linked by N—H···N and C—H···N hydrogen bonds into a two-dimensional network parallel to the (1 1 1) plane. The O—H···O and C—H···O hydrogen bonds (Table 1) involving the water molecules link the adjacent layers into a three-dimensional network. The crystal structure is further stablilized by C—H···π interactions involving the benzene ring (centroid Cg1).

Experimental

A solution of terepthaloyl chloride (203 mg, 1 mmol), in dry CH2Cl2 (20 ml) was put in a round bottle flask under nitrogen atmosphere. 2-Aminopyrimidine (190 mg, 2 mmol) containing triethylamine (0.55 ml) in dry CH2Cl2 (15 ml) was added dropwise. The reaction mixture was stirred at room temperature for 10 h. The reaction mixture was dried, washed with sodium bicarbonate solution, and then extracted with CH2Cl2 (4 × 20 ml). The crude mixture was purified by column chromatography (silica gel, 100–200 mesh) using 20% ethyl acetate-petroleum ether solution as eluent to afford a white solid compound (188 mg, 65%). Single crystals of the title compound were grown by slow evaporation of a CHCl3—CH3OH (3:1 v/v) solution (m.p. 457–459 K).

Refinement

All H atoms were located from the difference map and isotropically refined. One of the water hydrogen atoms is disordered over two positions with occupancies each 0.50. The O—H distances were restrained to be equal within 0.03 Å.

Figures

Fig. 1.
The molecular structure of the title compound, showing 60% probability displacement ellipsoids and the atomic numbering. One of the H atoms of the water molecule is disordered over two positions. The dashed line indicates a hydrogen bond. Atoms labelled ...
Fig. 2.
The crystal packing of the title compound, viewed along the a axis. Hydrogen bonds are shown as dashed lines.

Crystal data

C16H12N6O2·2H2OZ = 1
Mr = 356.35F000 = 186
Triclinic, P1Dx = 1.567 Mg m3
Hall symbol: -P 1Melting point = 457–459 K
a = 5.0733 (1) ÅMo Kα radiation λ = 0.71073 Å
b = 8.3233 (1) ÅCell parameters from 2202 reflections
c = 9.9622 (2) Åθ = 2.3–30.0º
α = 68.220 (1)ºµ = 0.12 mm1
β = 75.441 (1)ºT = 100.0 (1) K
γ = 82.333 (1)ºBlock, colourless
V = 377.720 (12) Å30.33 × 0.22 × 0.08 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2202 independent reflections
Radiation source: fine-focus sealed tube1982 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.035
Detector resolution: 8.33 pixels mm-1θmax = 30.0º
T = 100.0(1) Kθmin = 2.3º
ω scansh = −7→7
Absorption correction: multi-scan(SADABS; Bruker, 2005)k = −11→11
Tmin = 0.963, Tmax = 0.991l = −13→14
12751 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.044All H-atom parameters refined
wR(F2) = 0.106  w = 1/[σ2(Fo2) + (0.0387P)2 + 0.2638P] where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max = 0.001
2202 reflectionsΔρmax = 0.39 e Å3
154 parametersΔρmin = −0.26 e Å3
3 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods

Special details

Experimental. The data was collected with the Oxford Cyrosystem Cobra low-temperature attachment.
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.
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 > σ(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)

xyzUiso*/UeqOcc. (<1)
O10.40513 (19)0.85138 (12)0.21674 (10)0.0152 (2)
N10.7704 (2)0.64103 (14)−0.09155 (12)0.0131 (2)
N20.9113 (2)0.77862 (14)0.05021 (12)0.0134 (2)
N30.5215 (2)0.61544 (14)0.14450 (12)0.0124 (2)
H1N30.441 (4)0.530 (2)0.1395 (19)0.013 (4)*
C11.1248 (3)0.83918 (16)−0.06205 (14)0.0135 (2)
H11.248 (4)0.908 (2)−0.0464 (19)0.016 (4)*
C21.1741 (3)0.80284 (17)−0.19128 (14)0.0144 (2)
H21.328 (4)0.846 (2)−0.270 (2)0.018 (4)*
C30.9898 (3)0.70138 (17)−0.20052 (14)0.0144 (2)
H31.021 (4)0.669 (2)−0.287 (2)0.015 (4)*
C40.7440 (2)0.68481 (15)0.02820 (13)0.0113 (2)
C50.3775 (2)0.69938 (16)0.23761 (13)0.0121 (2)
C60.1803 (2)0.59197 (16)0.37078 (13)0.0114 (2)
C7−0.0689 (3)0.67033 (16)0.41794 (14)0.0131 (2)
H7−0.118 (4)0.789 (2)0.3599 (19)0.015 (4)*
C80.2492 (2)0.42173 (16)0.45293 (14)0.0126 (2)
H80.419 (4)0.368 (2)0.4211 (19)0.014 (4)*
O1W0.2790 (3)0.96683 (17)0.45548 (13)0.0296 (3)
H1W0.309 (5)0.934 (3)0.386 (2)0.034 (6)*
H2WA0.123 (6)0.994 (7)0.484 (6)0.050 (15)*0.50
H2WB0.380 (10)1.013 (7)0.479 (7)0.064 (18)*0.50

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0159 (4)0.0143 (4)0.0149 (4)−0.0037 (3)0.0011 (3)−0.0063 (3)
N10.0123 (5)0.0147 (5)0.0122 (5)−0.0017 (4)−0.0013 (4)−0.0054 (4)
N20.0125 (5)0.0142 (5)0.0132 (5)−0.0022 (4)−0.0009 (4)−0.0053 (4)
N30.0117 (5)0.0136 (5)0.0116 (5)−0.0040 (4)0.0014 (4)−0.0057 (4)
C10.0118 (5)0.0128 (5)0.0151 (6)−0.0018 (4)−0.0026 (4)−0.0040 (4)
C20.0110 (5)0.0168 (6)0.0128 (5)−0.0028 (4)0.0002 (4)−0.0035 (4)
C30.0134 (5)0.0179 (6)0.0116 (5)−0.0016 (4)−0.0009 (4)−0.0057 (5)
C40.0104 (5)0.0112 (5)0.0111 (5)−0.0006 (4)−0.0008 (4)−0.0033 (4)
C50.0108 (5)0.0148 (5)0.0105 (5)−0.0018 (4)−0.0013 (4)−0.0047 (4)
C60.0106 (5)0.0145 (5)0.0098 (5)−0.0035 (4)−0.0006 (4)−0.0052 (4)
C70.0127 (5)0.0140 (5)0.0123 (5)−0.0012 (4)−0.0014 (4)−0.0049 (4)
C80.0104 (5)0.0154 (5)0.0124 (5)−0.0014 (4)−0.0006 (4)−0.0064 (4)
O1W0.0388 (7)0.0353 (7)0.0186 (5)−0.0039 (5)−0.0004 (5)−0.0170 (5)

Geometric parameters (Å, °)

O1—C51.2252 (15)C3—H30.970 (18)
N1—C41.3429 (15)C5—C61.5006 (16)
N1—C31.3441 (16)C6—C81.3967 (17)
N2—C41.3325 (16)C6—C71.3976 (17)
N2—C11.3403 (16)C7—C8i1.3937 (17)
N3—C51.3734 (15)C7—H70.980 (18)
N3—C41.4037 (15)C8—C7i1.3937 (17)
N3—H1N30.886 (18)C8—H80.951 (18)
C1—C21.3850 (17)O1W—H1W0.807 (19)
C1—H10.976 (18)O1W—H2WA0.80 (2)
C2—C31.3810 (17)O1W—H2WB0.80 (2)
C2—H20.956 (18)
C4—N1—C3115.24 (10)N1—C4—N3115.16 (10)
C4—N2—C1115.74 (11)O1—C5—N3123.59 (11)
C5—N3—C4123.80 (10)O1—C5—C6120.82 (11)
C5—N3—H1N3117.2 (11)N3—C5—C6115.59 (10)
C4—N3—H1N3116.3 (11)C8—C6—C7120.14 (11)
N2—C1—C2122.42 (11)C8—C6—C5121.39 (11)
N2—C1—H1116.0 (10)C7—C6—C5118.30 (11)
C2—C1—H1121.5 (10)C8i—C7—C6119.91 (11)
C3—C2—C1116.73 (11)C8i—C7—H7119.9 (10)
C3—C2—H2121.6 (11)C6—C7—H7120.2 (10)
C1—C2—H2121.7 (11)C7i—C8—C6119.95 (11)
N1—C3—C2122.62 (11)C7i—C8—H8119.9 (11)
N1—C3—H3118.1 (11)C6—C8—H8120.2 (11)
C2—C3—H3119.3 (11)H1W—O1W—H2WA116 (4)
N2—C4—N1127.22 (11)H1W—O1W—H2WB128 (5)
N2—C4—N3117.53 (11)H2WA—O1W—H2WB111 (6)
C4—N2—C1—C2−1.83 (18)C4—N3—C5—O110.1 (2)
N2—C1—C2—C30.61 (19)C4—N3—C5—C6−169.50 (11)
C4—N1—C3—C2−0.68 (19)O1—C5—C6—C8−137.21 (13)
C1—C2—C3—N10.72 (19)N3—C5—C6—C842.36 (16)
C1—N2—C4—N11.96 (19)O1—C5—C6—C738.15 (17)
C1—N2—C4—N3178.50 (11)N3—C5—C6—C7−142.27 (12)
C3—N1—C4—N2−0.73 (19)C8—C6—C7—C8i−0.1 (2)
C3—N1—C4—N3−177.34 (11)C5—C6—C7—C8i−175.54 (11)
C5—N3—C4—N236.36 (18)C7—C6—C8—C7i0.1 (2)
C5—N3—C4—N1−146.68 (12)C5—C6—C8—C7i175.39 (11)

Symmetry codes: (i) −x, −y+1, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1W—H2WA···O1Wii0.80 (4)1.99 (4)2.791 (2)171 (6)
O1W—H1W···O10.81 (2)1.98 (2)2.785 (2)177 (3)
O1W—H2WB···O1Wiii0.80 (6)2.04 (5)2.795 (2)156 (6)
N3—H1N3···N1iv0.89 (2)2.14 (2)3.017 (2)169 (2)
C1—H1···N2v0.98 (2)2.61 (2)3.206 (2)119 (1)
C2—H2···O1Wv0.95 (2)2.58 (2)3.508 (2)164 (1)
C3—H3···Cg1vi0.97 (2)2.98 (2)3.914 (2)164 (2)
C3—H3···Cg1iv0.97 (2)2.98 (2)3.914 (2)164 (2)

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

Footnotes

1This paper is dedicated to His Majesty, Thai King Bhumibol Adulyadej on the occasion of his 80th Birthday Anniversary which fell on December 5th, 2007.

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI2534).

References

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