Experimental. Crystal data

Transcription

1 organic compounds Acta Crystallographica Section E Structure Reports Online ISSN Bis[8-ethyl-5-oxo-2-(piperazin-4-ium-1- yl)-5,8-dihydropyrido[2,3-d]pyrimidine- 6-carboxylic acid] 2,5-dicarboxybenzene-1,4-dicarboxylate octahydrate Guang-Ju Zhang,* Jiang-Hong He, Shi-Wei Yan, Zhong-Li Ye and Guang-Hua Xin College of Chemistry and Chemical Engineering, Southwest University, Chongqing,400715, People s Republic of China Correspondence guaiguaijuzi@yahoo.com.cn Received 19 March 2011; accepted 25 March 2011 Key indicators: single-crystal X-ray study; T = 296 K; mean (C C) = Å; R factor = 0.046; wr factor = 0.160; data-to-parameter ratio = Experimental Crystal data C 14 H 18 N 5 O C 10 H 4 O 8 4H 2 O M r = Triclinic, P1 a = (16) Å b = (2) Å c = (2) Å = (2) = (2) Data collection Bruker SMART APEX CCD areadetector diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 1996) T min = 0.940, T max = Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections 352 parameters 14 restraints = (2) V = (4) Å 3 Z =2 Mo K radiation = 0.12 mm 1 T = 296 K mm measured reflections 5071 independent reflections 3550 reflections with I > 2(I) R int = H atoms treated by a mixture of independent and constrained refinement max = 0.33 e Å 3 min = 0.20 e Å 3 The asymmetric unit of the title compound, 2C 14 H 18 N 5 O C 10 H 5 O 8 2 8H 2 O, contains one [H 2 ppa] + cation, one half of an [H 2 btec] 2 anion (H 4 btec = 1,2,4,5-benzenetetracarboxylic acid and Hppa = 8-ethyl-5-oxo-2-piperazin-1-yl-5,8-dihydropyrido[2,3-d]pyrimidine-6-carboxylic acid) that is completed by inversion symmetry and four water molecules. In the crystal, the molecules are connected by intermolecular hydrogen-bonding interactions and stacking between the benzene rings of the [H 2 btec] 2 anion and the pyrimidine rings of the [H 2 ppa] + cation [centroid centroid distance = (3) Å], generating a three-dimensional supramolecular structure. Related literature For general background to the use of quinolones in the treatment of infections, see: Mizuki et al. (1996). Table 1 Hydrogen-bond geometry (Å, ). D HA D H HA DA D HA O6 H6AO4 i 0.92 (2) 1.47 (2) (2) 178 (3) N1 H1AOW1 ii (2) 164 N1 H1AO6 ii (2) 113 N1 H1BOW2 ii (2) 176 OW1 HW1AO1 iii 0.88 (2) 1.98 (2) (2) 150 (2) OW1 HW1BO (2) 2.38 (2) (2) 135 (2) OW1 HW1BO (2) 2.57 (2) (2) 132 (2) OW1 HW1BO (2) 2.59 (2) (2) 118 (2) O2 H2AO (2) 1.56 (2) (19) 159 (2) OW2 HW2BOW4 iv 0.86 (2) 1.86 (2) (3) 168 (3) OW2 HW2AO5 iv 0.84 (2) 1.98 (2) (2) 173 (3) OW3 HW3AOW1 v 0.85 (2) 1.93 (2) (2) 169 (3) OW3 HW3BO2 vi 0.85 (2) 2.17 (2) (3) 172 (3) OW4 HW4AO4 vii 0.87 (2) 1.94 (2) (2) 163 (3) OW4 HW4BOW (2) 1.97 (2) (3) 174 (3) Symmetry codes: (i) x; y þ 2; z þ 1; (ii) x; y; z 1; (iii) x þ 1; y; z; (iv) x þ 1; y þ 2; z þ 1; (v) x þ 1; y þ 1; z þ 1; (vi) x þ 1; y; z 1; (vii) x þ 1; y þ 2; z. Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL-Plus (Sheldrick, 2008); software used to prepare material for publication: SHELXL97. This work was supported by the Science and Technology Foundation of Southwest University (SWUB ). Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FF2005). Acta Cryst. (2011). E67, o1011 o1012 doi: /s Zhang et al. o1011

2 organic compounds References Bruker (2001). SMART and SAINT. Bruker AXS Inc., Madison Wisconsion, USA. Mizuki, Y., Fujiwara, I. & Yamaguchi, T. (1996). J. Antimicrob. Chemother. Suppl. A, 37, Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany. Sheldrick, G. M. (2008). Acta Cryst. A64, o1012 Zhang et al. C 14 H 18 N 5 O C 10 H 4 O 8 4H 2 O Acta Cryst. (2011). E67, o1011 o1012

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4 Acta Cryst. (2011). E67, o1011-o1012 [ doi: /s ] Bis[8-ethyl-5-oxo-2-(piperazin-4-ium-1-yl)-5,8-dihydropyrido[2,3-d]pyrimidine-6-carboxylic acid] 2,5-dicarboxybenzene-1,4-dicarboxylate octahydrate G.-J. Zhang, J.-H. He, S.-W. Yan, Z.-L. Ye and G.-H. Xin Comment Pipemidic acid (8-ethyl-5-oxo-2-piperazin-1-yl-5,8-dihydropyrido[2,3-d]pyrimidine-6- carboxylic acid) is member of quinolones used to treat infections (Mizuki et al., 1996). The complexes of the Hppa and H 4 btec have not been reported till now. In this paper, the structure of the title compound, 1, is described (Fig. 1). The asymmetric unit contains one [H 2 ppa] + cation, one half of [H 2 btec] 2- anion that is completed by inversion symmetry, and four lattice water molecules. The molecules are linked by intermolecular N H O and O H O hydrogen-bonding interactions (N O = (2) (2) Å, O O = (2) (2) Å) and π π stacking between the benzene rings of [H 2 btec] 2- anion and the pyrimidine rings of [H 2 ppa] + cation (centroid distance of (3) Å) to form a three-dimensional supramolecular structure. Experimental A mixture of AgNO 3 (0.085 g, 0.5 mmol), Hppa (0.089 g, 0.25 mmol), H 4 btec (0.064 g, 0.25 mmol) and distilled water (8 ml) was stirred for 20 min. in air. The mixture was then transferred to a 18 ml Teflon-lined hydrothermal bomb. The bomb was kept at 393 K for 96 h under autogenous pressure. Upon cooling, colorless blocks of 1 were obtained from the reaction mixture. Refinement The H atoms bonded to C atoms were positioned geometrically and refined using a riding model approximation [aromatic C H = 0.93 Å, aliphatic C H = Å], with U iso (H) = Ueq(C).The H on N atoms were located in difference Fourier maps, and refined with distances restraint of N H = 0.90 Å, and with U iso (H)= 1.2 U eq (N). The H atoms bonded to O atoms were located in difference Fourier maps and refined with Uiso(H) = 1.3 Ueq(O) for carboxyl groups of [C 14 H 18 O 3 N 5 ] + and [C 10 H 4 O 8 ] 2- respectively. The O H bonds are Å and Å in carboxyl groups of [C 14 H 18 O 3 N 5 ] + and [C 10 H 4 O 8 ] 2-. The H atoms bonded to OW atoms were located in a difference Fourier maps and refined with OW H =0.812 Å Å and U iso (H) = U eq (OW). sup-1

5 Figures Fig. 1. The structure of 1. Displacement ellipsoids are drawn at the 30% probability level. H atoms have been omitted for clarity. [Symmetry code: -x,-y+2, -z+1]. Bis[8-ethyl-5-oxo-2-(piperazin-4-ium-1-yl)-5,8-dihydropyrido[2,3- d]pyrimidine-6-carboxylic acid] 2,5-dicarboxybenzene-1,4-dicarboxylate octahydrate Crystal data C 14 H 18 N 5 O C 10 H 4 O 8 4H 2 O Z = 2 M r = F(000) = 530 Triclinic, P1 D x = Mg m 3 Hall symbol: -P 1 Mo Kα radiation, λ = Å a = (16) Å Cell parameters from reflections b = (2) Å θ = c = (2) Å µ = 0.12 mm 1 α = (2) T = 296 K β = (2) Block, colourless γ = (2) mm V = (4) Å 3 Data collection Bruker APEX CCD area-detector diffractometer Radiation source: fine-focus sealed tube graphite R int = independent reflections 3550 reflections with I > 2σ(I) phi and ω scans θ max = 27.4, θ min = 2.5 Absorption correction: multi-scan (SADABS; Sheldrick, 1996) T min = 0.940, T max = h = k = measured reflections l = Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H atoms treated by a mixture of independent and constrained refinement sup-2

6 S = 1.01 w = 1/[σ 2 (F 2 o ) + (0.1P) 2 ] where P = (F 2 o + 2F 2 c )/ reflections (Δ/σ) max < parameters Δρ max = 0.33 e Å 3 14 restraints Δρ min = 0.20 e Å 3 Special details 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 F 2 against ALL reflections. The weighted R-factor wr and goodness of fit S are based on F 2, conventional R-factors R are based on F, with F set to zero for negative F 2. The threshold expression of F 2 > σ(f 2 ) is used only for calculating R- factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 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 (Å 2 ) x y z U iso */U eq C (2) (18) (14) (4) C (2) (16) (13) (4) C (2) (15) (13) (4) C (18) (14) (12) (3) C (2) (16) (13) (4) H5A * C (19) (16) (13) (4) C (18) (14) (12) (3) C (2) (16) (13) (4) H8A * C (19) (17) (14) (4) H9A * H9B * C (3) (2) (2) (6) H10A * H10B * H10C * C (2) (19) (14) (4) H11A * H11B * C (2) (19) (14) (5) H12A * H12B * C (2) (19) (14) (5) H13A * H13B * C (2) (2) (15) (5) sup-3

7 H14A * H14B * C (2) (15) (12) (4) C (2) (15) (14) (4) H (2) (16) (15) (5)* C (19) (15) (12) (4) C (2) (16) (14) (4) C (2) (18) (15) (4) N (18) (15) (11) (4) H1A * H1B * N (17) (15) (11) (4) N (16) (14) (11) (3) N (15) (13) (10) (3) N (15) (13) (11) (3) O (18) (16) (11) (4) OW (19) (15) (12) (4) HW1A (19) (2) (18) 0.072* HW1B (2) (2) (16) 0.070* O (19) (15) (12) (4) H2A (2) (2) (19) (8)* OW (2) (17) (14) (5) HW2A (3) (3) (18) 0.097* HW2B (3) (2) (19) 0.103* O (15) (12) (10) (3) OW (3) (18) (17) (5) HW3A (3) (3) (17) 0.092* HW3B (4) (3) (15) 0.118* OW (2) (17) (14) (5) HW4A (4) (2) (15) 0.107* HW4B (3) (16) (2) 0.092* O (18) (16) (11) (4) O (16) (14) (12) (4) O (2) (16) (11) (4) H6A (2) (2) (2) (8)* O (18) (16) (13) (5) Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 C (11) (11) (9) (9) (8) (8) C (9) (9) (8) (7) (7) (7) C (9) (8) (8) (7) (7) (6) C (8) (8) (8) (6) (6) (6) C (8) (10) (9) (7) (7) (7) C (8) (9) (8) (7) (6) (7) C (8) (8) (7) (6) (6) (6) C (8) (10) (8) (7) (6) (7) sup-4

8 C (8) (10) (9) (7) (7) (7) C (13) (13) (15) (10) (12) (11) C (10) (11) (9) (8) (7) (8) C (10) (12) (9) (9) (8) (8) C (10) (12) (10) (9) (8) (8) C (9) (13) (9) (9) (7) (8) C (9) (8) (8) (7) (6) (6) C (8) (9) (9) (7) (7) (7) C (9) (8) (8) (7) (6) (6) C (10) (9) (9) (8) (7) (7) C (11) (11) (10) (9) (8) (8) N (9) (9) (7) (7) (6) (6) N (8) (10) (7) (7) (6) (7) N (7) (9) (7) (6) (6) (6) N (7) (8) (7) (6) (5) (6) N (7) (8) (7) (6) (5) (5) O (9) (11) (7) (8) (6) (7) OW (9) (10) (9) (8) (7) (7) O (10) (10) (7) (8) (7) (7) OW (11) (11) (10) (9) (8) (8) O (8) (8) (7) (6) (6) (6) OW (14) (13) (12) (11) (11) (10) OW (13) (11) (9) (10) (9) (9) O (10) (12) (7) (8) (6) (7) O (8) (9) (8) (7) (6) (7) O (10) (11) (7) (9) (7) (7) O (9) (12) (9) (8) (7) (8) Geometric parameters (Å, ) C1 O (2) C12 H12B C1 O (2) C13 N (2) C1 C (2) C13 C (3) C2 C (2) C13 H13A C2 C (2) C13 H13B C3 O (2) C14 N (2) C3 C (2) C14 H14A C4 C (2) C14 H14B C4 C (2) C15 C (2) C5 N (2) C15 C17 i (2) C5 H5A C15 C (2) C6 N (2) C16 C (2) C6 N (2) C16 H (19) C6 N (2) C17 C15 i (2) C7 N (19) C17 C (2) C7 N (19) C18 O (2) C8 N (2) C18 O (2) C8 H8A C19 O (2) C9 N (2) C19 O (2) sup-5

9 C9 C (3) N1 H1A C9 H9A N1 H1B C9 H9B OW1 HW1A (15) C10 H10A OW1 HW1B (15) C10 H10B O2 H2A (16) C10 H10C OW2 HW2A (16) C11 N (2) OW2 HW2B (16) C11 C (3) OW3 HW3A (16) C11 H11A OW3 HW3B (17) C11 H11B OW4 HW4A (16) C12 N (2) OW4 HW4B (16) C12 H12A O6 H6A (17) O1 C1 O (17) N1 C13 C (15) O1 C1 C (18) N1 C13 H13A O2 C1 C (16) C14 C13 H13A C8 C2 C (14) N1 C13 H13B C8 C2 C (16) C14 C13 H13B C3 C2 C (15) H13A C13 H13B O3 C3 C (15) N2 C14 C (14) O3 C3 C (15) N2 C14 H14A C2 C3 C (14) C13 C14 H14A C7 C4 C (14) N2 C14 H14B C7 C4 C (14) C13 C14 H14B C5 C4 C (15) H14A C14 H14B N3 C5 C (15) C16 C15 C17 i (15) N3 C5 H5A C16 C15 C (15) C4 C5 H5A C17 i C15 C (15) N4 C6 N (15) C17 C16 C (15) N4 C6 N (14) C17 C16 H (11) N2 C6 N (14) C15 C16 H (11) N4 C7 N (13) C16 C17 C15 i (14) N4 C7 C (14) C16 C17 C (15) N5 C7 C (14) C15 i C17 C (15) N5 C8 C (15) O5 C18 O (16) N5 C8 H8A O5 C18 C (16) C2 C8 H8A O4 C18 C (16) N5 C9 C (15) O7 C19 O (18) N5 C9 H9A O7 C19 C (17) C10 C9 H9A O6 C19 C (17) N5 C9 H9B C13 N1 C (13) C10 C9 H9B C13 N1 H1A H9A C9 H9B C12 N1 H1A C9 C10 H10A C13 N1 H1B C9 C10 H10B C12 N1 H1B H10A C10 H10B H1A N1 H1B C9 C10 H10C C6 N2 C (14) H10A C10 H10C C6 N2 C (15) H10B C10 H10C C11 N2 C (13) sup-6

10 N2 C11 C (15) C5 N3 C (14) N2 C11 H11A C7 N4 C (14) C12 C11 H11A C8 N5 C (14) N2 C11 H11B C8 N5 C (13) C12 C11 H11B C7 N5 C (13) H11A C11 H11B HW1A OW1 HW1B (17) N1 C12 C (14) C1 O2 H2A (15) N1 C12 H12A HW2A OW2 HW2B 107 (2) C11 C12 H12A HW3A OW3 HW3B 106 (2) N1 C12 H12B HW4A OW4 HW4B 109 (2) C11 C12 H12B C19 O6 H6A (16) H12A C12 H12B Symmetry codes: (i) x, y+2, z+1. Hydrogen-bond geometry (Å, ) D H A D H H A D A D H A O6 H6A O4 i 0.92 (2) 1.47 (2) (2) 178 (3) N1 H1A OW1 ii (2) 164 N1 H1A O6 ii (2) 113 N1 H1B OW2 ii (2) 176 OW1 HW1A O1 iii 0.88 (2) 1.98 (2) (2) 150 (2) OW1 HW1B O (2) 2.38 (2) (2) 135.(2) OW1 HW1B O (2) 2.57 (2) (2) 132.(2) OW1 HW1B O (2) 2.59 (2) (2) 118 (2) O2 H2A O (2) 1.56 (2) (19) 159 (2) OW2 HW2B OW4 iv 0.86 (2) 1.86 (2) (3) 168 (3) OW2 HW2A O5 iv 0.84 (2) 1.98 (2) (2) 173 (3) OW3 HW3A OW1 v 0.85 (2) 1.93 (2) (2) 169 (3) OW3 HW3B O2 vi 0.85 (2) 2.17 (2) (3) 172 (3) OW4 HW4A O4 vii 0.87 (2) 1.94 (2) (2) 163 (3) OW4 HW4B OW (2) 1.97 (2) (3) 174 (3) Symmetry codes: (i) x, y+2, z+1; (ii) x, y, z 1; (iii) x+1, y, z; (iv) x+1, y+2, z+1; (v) x+1, y+1, z+1; (vi) x+1, y, z 1; (vii) x+1, y+2, z. sup-7

11 Fig. 1 sup-8