data reports Structure description

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1 ISSN [2,4-Dihydroxy-5-(5-hydroxy-2,4,6-trioxo-3,5-di- hydro-1h-pyrimidin-5-yl)-3-methoxyphenyl]-5- hydroxy-3,5-dihydro-1h-pyrimidine-2,4,6-trione pentahydrate Received 7 February 2016 Accepted 14 February 2016 Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland Keywords: crystal structure; ion-pair recognition; alloxan; vasarene analogues; supramolecular ligand; hydrogen bonding; threedimensional supramolecular structure. CCDC reference: Ravell Bengiat, a Asne Klein, a Maayan Gil, a Benny Bogoslavsky, a Shmuel Cohen, a Guy Yardeni, b Israel Zilbermann b and Joseph Almog a * a Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, , Israel, and b Department of Chemistry, The Nuclear Research Centre Negev, Beer Sheva, 84190, Israel. *Correspondence almog@mail.huji.ac.il The title compound, C 15 H 12 N 4 O 11 5H 2 O, has a propeller-like structure. The two alloxan units have screw-boat conformations. Their mean planes are normal to the central aromatic ring with dihedral angles of (7) and (7),and they are inclined to one another by (7). In the crystal, molecules are linked via O HO and N HO hydrogen bonds, forming a threedimensional framework. There are also C HO hydrogen bonds present within the framework. Structural data: full structural data are available from iucrdata.iucr.org Structure description Vasarene and analogues are prepared by a one-pot reaction between cyclic vicinal polycarbonyl compounds, such as ninhydrin and benzo[f]ninhydrin (Almog et al., 2009), and polyhydroxy aromatics. Previous work by our group (Almog et al., 2009) has shown that the reaction with alloxan (1,3-dihydropyrimidine-2,4,5,6-tetrone) results in a partially closed, propeller-like structure, where the alloxan units are in a perpendicular and slightly tilted position (40 60 ), due to the tetrahedral angle of the sp 3 carbon atom of the alloxan attached to the central aromatic ring. Attempts to prepare bis-adducts with other polyhydroxy aromatics have also been successful, following a similar pattern. These compounds have shown promising potential for the challenging task of selective precipitation of certain alkali fluorides from aqueous solutions. The molecular structure of the title compound is illustrated in Fig. 1. A selective methylation on the central hydroxyl group of the 1,2,3-benzenetriol molecule was 1of3

2 Table 1 Hydrogen-bond geometry (Å, ). D HA D H HA DA D HA O1 H1OO1W i 0.81 (3) 1.97 (2) (18) 148 (2) O3 H3OO (3) 2.41 (2) (16) 112 (2) O3 H3OO2W ii 0.75 (3) 2.12 (3) (18) 147 (2) O4 H4OO9 iii 0.83 (2) 1.93 (2) (16) 168 (2) O8 H8OO6 iv 0.87 (3) 2.13 (2) (16) 140 (2) O8 H8OO4W v 0.87 (3) 2.63 (3) (19) 129 (2) N1 H1NO2W 0.92 (2) 1.97 (2) (19) 169 (2) N2 H2NO1W vi 0.89 (2) 1.92 (2) (18) (18) N3 H3NO3W vii 0.82 (3) 2.00 (3) (19) 167 (2) N4 H4NO4W vii 0.82 (2) 2.13 (2) (19) 158 (2) O1W H11WO10 ii 0.87 (2) 1.97 (2) (18) 161 (3) O1W H21WO5W 0.90 (2) 1.77 (2) (3) 164 (2) O2W H12WO5 viii 0.85 (2) 2.23 (2) (19) 165 (3) O2W H22WO4W 0.84 (2) 1.98 (2) (2) 175 (3) O3W H13WO7 vi 0.86 (2) 2.30 (2) (18) 147 (3) O3W H13WO (2) 2.44 (2) (19) 126 (3) O3W H23WO4 ix 0.83 (2) 2.10 (2) (18) 178 (3) O4W H14WO3W v 0.84 (2) 1.97 (2) (2) 178 (3) O4W H24WO11 viii 0.83 (2) 2.08 (2) (18) 168 (3) O5W H15WO (3) 164 O5W H25WO (3) 139 C7 H7BO7 i (2) 151 C7 H7BO11 x (2) 125 C7 H7CO10 ii (2) 159 Symmetry codes: (i) x; y; z þ 1; (ii) x þ 1; y þ 1; z þ 1; (iii) x; y; z; (iv) x þ 1; y þ 1; z; (v) x þ 1; y þ 1; z; (vi) x; y þ 1; z; (vii) x 1; y 1; z; (viii) x þ 1; y; z; (ix) x; y þ 1; z; (x) x; y þ 1; z þ 1. performed prior to the one-pot reaction with alloxan. It can be used as a model for potential binding to a solid phase for future separation techniques. The title compound, contains several oxygen and nitrogen functional groups (hydroxyls, carbonyls and amides) that are capable of forming multiple hydrogen bonds with protic solvent molecules (Table 1 and Figs. 2 and 3). This greatly enhances its solubility in water, thus enabling the selective binding and precipitation of the highly soluble heavy alkali fluorides from aqueous solutions, as shall be reported in a forthcoming article, and exhibiting promising potential as a new analytical method for salt-separation techniques. The Figure 2 A partial view of the crystal packing of the title compound, showing some of the hydrogen bonds involving the water molecules (dashed lines; see Table 1). Displacement ellipsoids are drawn at the 50% probability level. propeller-like structure is established as non-hemiketal ring closure is allowed with a second carbonyl group, unlike the ninhydrin-based vasarene analogues (Almog et al., 2016). We suspect that this is due to two main factors: 1) the less reactive amidic carbonyls compared to the true ketones on ninhydrin; 2) a greater ring strain when closing a six-membered ring compared to the five-membered ring of ninhydrin. Nevertheless, this structure is responsible for the greater flexibility of the ligand as opposed to the rigid ninhydrin-based vasarenes, assisting in the final complex formation with alkali fluoride ion-pairs. Synthesis and crystallization Alloxan monohydrate (329 mg, 2.05 mmol) and 2-methoxybenzene-1,3-diol (prepared according to a known procedure; Donnelly et al., 2008) (142 mg, 1.01 mmol) were stirred at room temperature in glacial acetic acid (10 ml) for 24 h. The white precipitate that formed was collected by vacuum filtration. The filtrate was left sealed and after a few days colourless crystals were formed. They were filtered onto sintered glass Figure 1 A view of the molecular structure of the title compound, with the atom labelling. Displacement ellipsoids are drawn at the 50% probability level. All solvent molecules have been omitted for clarity. Figure 3 A perspective view along the a axis of the crystal packing of the title compound. The hydrogen bonds are shown as dashed lines (see Table 1), and C-bound H atoms have been omitted for clarity. 2of3 Bengiat et al. C 15 H 12 N 4 O 11 5H 2 O

3 Table 2 Experimental details. Crystal data Chemical formula C 15 H 12 N 4 O 11 5H 2 O M r Crystal system, space group Triclinic, P1 Temperature (K) 295 a, b, c (Å) (6), (6), (8),, ( ) (1), (1), (1) V (Å 3 ) (11) Z 2 Radiation type Mo K (mm 1 ) 0.15 Crystal size (mm) Data collection Diffractometer Bruker APEXII CCD areadetector Absorption correction Multi-scan (SADABS; Bruker, 2010) T min, T max 0.939, No. of measured, independent and 12041, 4821, 4337 observed [I > 2(I)] reflections R int (sin /) max (Å 1 ) Refinement R[F 2 >2(F 2 )], wr(f 2 ), S 0.045, 0.133, 1.04 No. of reflections 4821 No. of parameters 381 No. of restraints 12 H-atom treatment H atoms treated by a mixture of independent and constrained refinement max, min (e Å 3 ) 0.35, 0.44 Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SHELXS97 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008), SHELXTL (Sheldrick, 2008). and washed with AcOH followed by diethyl ether (yield: 103 mg, 24%). Recrystallization (MeOH/H 2 O) afforded colourless crystals (m.p. > 473 K with decomposition). Analysis calculated for C 15 H 12 N 4 O 11 +2H 2 O: C, 39.14; H, 3.50; N, 12.17; found: C, 39.35; H, 3.29; N, 11.90; 1 H NMR (DMSOd 6 ) (p.p.m.): 3.49 (s, 3H), 7.35 (br s, 2H), 7.62 (s,1h),9.45(br s, 2H), (br s, 4H); UV/Vis (DMSO): max = 282 nm. IR: = 494, 527, 606, 702, 793, 1020, 1132, 1246, 1348, 1411, 1479, 1699, 2842, 3101, 3209, 3300, 3373 cm 1 ; MS/MS positive mode ESI (m/z): [(M +H)-H 2 O] +, [M +NH 4 ] +, [M + Na] +, [2M + Na] +. Refinement Crystal data, data collection and structure refinement details are summarized in Table 2. Acknowledgements This research was supported by the Pazy Research Foundation. References Almog, J., Bengiat, R., Gil, M., Klein, A., Cohen, O., Bogoslavski, B., Cohen, S. & Dubnikova, F. (2016). Tetrahedron. Submitted. Almog, J., Rozin, R., Klein, A., Shamuilov-Levinton, G. & Cohen, S. (2009). Tetrahedron, 65, Bruker (2010). APEX2, SAINT, and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Donnelly, A. C., Mays, J. R., Burlison, J., Nelson, J. T., Vielhauer, G., Holzbeierlein, J. & Blagg, B. S. J. (2008). J. Org. Chem. 73, 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, Sheldrick, G. M. (2008). Acta Cryst. A64, Sheldrick, G. M. (2015). Acta Cryst. C71, 3 8. Bengiat et al. C 15 H 12 N 4 O 11 5H 2 O 3of3

4 full crystallographic data [ 5-[2,4-Dihydroxy-5-(5-hydroxy-2,4,6-trioxo-3,5-dihydro-1H-pyrimidin-5-yl)-3- methoxyphenyl]-5-hydroxy-3,5-dihydro-1h-pyrimidine-2,4,6-trione pentahydrate Ravell Bengiat, Asne Klein, Maayan Gil, Benny Bogoslavsky, Shmuel Cohen, Guy Yardeni, Israel Zilbermann and Joseph Almog 5-[2,4-Dihydroxy-5-(5-hydroxy-2,4,6-trioxo-1,3-diazinan-5-yl)-3-methoxyphenyl]-5-hydroxy-1,3- diazinane-2,4,6-trione pentahydrate Crystal data C 15 H 12 N 4 O 11 5H 2 O M r = Triclinic, P1 a = (6) Å b = (6) Å c = (8) Å α = (1) β = (1) γ = (1) V = (11) Å 3 Data collection Bruker APEXII CCD area-detector diffractometer Radiation source: fine-focus sealed tube Graphite monochromator phi and ω scans Absorption correction: multi-scan (SADABS; Bruker, 2010) T min = 0.939, T max = Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = S = reflections 381 parameters 12 restraints Primary atom site location: structure-invariant direct methods Z = 2 F(000) = 536 D x = Mg m 3 Mo Kα radiation, λ = Å Cell parameters from 6750 reflections θ = µ = 0.15 mm 1 T = 295 K Plate, colourless mm measured reflections 4821 independent reflections 4337 reflections with I > 2σ(I) R int = θ max = 27.9, θ min = 1.8 h = k = l = Secondary atom site location: difference Fourier map Hydrogen site location: mixed H atoms treated by a mixture of independent and constrained refinement w = 1/[σ 2 (F o2 ) + (0.0802P) P] where P = (F o 2 + 2F c2 )/3 (Δ/σ) max < Δρ max = 0.35 e Å 3 Δρ min = 0.44 e Å 3 data-1

5 Special details 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. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 ) x y z U iso */U eq O (13) (13) (11) (3) H1O (3) (3) (2) (6)* O (13) (12) (9) (2) O (13) (12) (10) (3) H3O (3) (3) (2) (6)* O (13) (12) (9) (3) H4O (3) (3) (2) (6)* O (15) (14) (16) (4) O (13) (12) (11) (3) O (12) (13) (11) (3) O (12) (12) (9) (3) H8O (3) (3) (2) (6)* O (14) (13) (12) (3) O (16) (15) (14) (4) O (13) (13) (11) (3) N (15) (14) (12) (3) H1N (3) (3) (2) (6)* N (14) (14) (12) (3) H2N (2) (2) (17) (5)* N (15) (15) (13) (3) H3N (3) (3) (2) (6)* N (14) (14) (11) (3) H4N (3) (3) (2) (6)* C (15) (15) (12) (3) C (15) (15) (12) (3) C (16) (15) (12) (3) C (15) (15) (12) (3) C (15) (14) (12) (3) C (15) (15) (12) (3) H * C (2) (2) (15) (4) H7A * H7B * H7C * C (15) (15) (12) (3) C (17) (17) (15) (3) C (16) (16) (13) (3) C (16) (15) (12) (3) C (15) (15) (12) (3) data-2

6 C (16) (16) (14) (3) C (18) (17) (15) (3) C (16) (15) (13) (3) O1W (17) (14) (12) (3) H11W (3) (2) (2) (10)* H21W (3) (3) (18) (8)* O2W (15) (14) (11) (3) H12W (3) (19) (2) (9)* H22W (3) (3) (2) (8)* O3W (14) (16) (12) (3) H13W (3) (4) (2) (10)* H23W (4) (3) (3) (10)* O4W (15) (15) (14) (3) H14W (3) (2) (19) (7)* H24W (2) (3) (2) (8)* O5W (3) (3) (2) (7) H15W * H25W * Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 O (6) (6) (6) (5) (5) (5) O (6) (6) (5) (5) (4) (4) O (6) (6) (5) (4) (4) (4) O (6) (5) (5) (5) (4) (4) O (7) (6) (13) (5) (7) (7) O (6) (6) (7) (5) (5) (5) O (6) (6) (7) (4) (5) (5) O (6) (6) (5) (4) (4) (4) O (6) (6) (8) (5) (5) (5) O (7) (7) (9) (6) (6) (6) O (6) (6) (7) (5) (5) (5) N (6) (6) (7) (5) (5) (5) N (6) (6) (7) (5) (5) (5) N (6) (7) (8) (5) (5) (6) N (6) (6) (7) (5) (5) (5) C (6) (6) (7) (5) (5) (5) C (7) (6) (7) (5) (5) (5) C (7) (6) (6) (5) (5) (5) C (6) (6) (6) (5) (5) (5) C (6) (6) (6) (5) (5) (5) C (6) (6) (6) (5) (5) (5) C (10) (9) (8) (8) (7) (7) C (6) (6) (7) (5) (5) (5) C (7) (7) (9) (6) (6) (6) C (7) (6) (7) (5) (5) (5) C (7) (6) (6) (5) (5) (5) data-3

7 C (6) (6) (7) (5) (5) (5) C (7) (6) (8) (5) (6) (6) C (7) (7) (8) (6) (6) (6) C (7) (6) (7) (5) (5) (5) O1W (8) (6) (7) (6) (6) (5) O2W (7) (6) (7) (5) (5) (5) O3W (6) (8) (8) (6) (6) (6) O4W (7) (7) (9) (5) (6) (6) O5W (17) (15) (17) (13) (13) (13) Geometric parameters (Å, º) O1 C (17) N4 H4N 0.82 (2) O1 H1O 0.81 (3) C1 C (19) O2 C (17) C1 C (2) O2 C (2) C1 C (18) O3 C (17) C2 C (19) O3 H3O 0.75 (3) C3 C (19) O4 C (17) C4 C (19) O4 H4O 0.83 (2) C5 C (18) O5 C (2) C5 C (18) O6 C (17) C6 H O7 C (19) C7 H7A O8 C (17) C7 H7B O8 H8O 0.87 (3) C7 H7C O9 C (19) C8 C (19) O10 C (2) C8 C (2) O11 C (19) C12 C (19) N1 C (2) C12 C (2) N1 C (2) O1W H11W (17) N1 H1N 0.92 (2) O1W H21W (16) N2 C (19) O2W H12W (17) N2 C (2) O2W H22W (16) N2 H2N 0.89 (2) O3W H13W (17) N3 C (2) O3W H23W (17) N3 C (19) O4W H14W (16) N3 H3N 0.82 (3) O4W H24W (17) N4 C (18) O5W H15W N4 C (2) O5W H25W C2 O1 H1O (16) O2 C7 H7C C3 O2 C (12) H7A C7 H7C C4 O3 H3O (18) H7B C7 H7C C8 O4 H4O (15) O4 C8 C (11) C12 O8 H8O (16) O4 C8 C (12) C13 N1 C (14) C1 C8 C (11) C13 N1 H1N (14) O4 C8 C (12) C14 N1 H1N (15) C1 C8 C (12) data-4

8 C15 N2 C (13) C11 C8 C (11) C15 N2 H2N (13) O5 C9 N (15) C14 N2 H2N (13) O5 C9 C (14) C10 N3 C (14) N3 C9 C (13) C10 N3 H3N (16) O6 C10 N (14) C9 N3 H3N (16) O6 C10 N (14) C11 N4 C (13) N3 C10 N (12) C11 N4 H4N (16) O7 C11 N (14) C10 N4 H4N (16) O7 C11 C (13) C6 C1 C (12) N4 C11 C (12) C6 C1 C (13) O8 C12 C (11) C2 C1 C (12) O8 C12 C (12) O1 C2 C (13) C5 C12 C (11) O1 C2 C (12) O8 C12 C (12) C3 C2 C (12) C5 C12 C (11) O2 C3 C (13) C15 C12 C (11) O2 C3 C (12) O9 C13 N (14) C2 C3 C (13) O9 C13 C (13) O3 C4 C (13) N1 C13 C (13) O3 C4 C (12) O10 C14 N (15) C3 C4 C (12) O10 C14 N (16) C6 C5 C (12) N2 C14 N (14) C6 C5 C (12) O11 C15 N (14) C4 C5 C (12) O11 C15 C (13) C1 C6 C (13) N2 C15 C (13) C1 C6 H H11W O1W H21W 97.9 (19) C5 C6 H H12W O2W H22W 103 (2) O2 C7 H7A H13W O3W H23W 106 (2) O2 C7 H7B H14W O4W H24W 107 (2) H7A C7 H7B H15W O5W H25W C6 C1 C2 O (13) C9 N3 C10 N4 0.5 (2) C8 C1 C2 O1 0.9 (2) C11 N4 C10 O (14) C6 C1 C2 C3 0.2 (2) C11 N4 C10 N3 4.1 (2) C8 C1 C2 C (13) C10 N4 C11 O (14) C7 O2 C3 C (17) C10 N4 C11 C8 6.9 (2) C7 O2 C3 C (17) O4 C8 C11 O (16) O1 C2 C3 O2 1.5 (2) C1 C8 C11 O (18) C1 C2 C3 O (12) C9 C8 C11 O (14) O1 C2 C3 C (13) O4 C8 C11 N (14) C1 C2 C3 C4 1.1 (2) C1 C8 C11 N (13) O2 C3 C4 O3 2.1 (2) C9 C8 C11 N (18) C2 C3 C4 O (13) C6 C5 C12 O (17) O2 C3 C4 C (12) C4 C5 C12 O (13) C2 C3 C4 C5 0.1 (2) C6 C5 C12 C (13) O3 C4 C5 C (13) C4 C5 C12 C (18) C3 C4 C5 C6 1.6 (2) C6 C5 C12 C (14) O3 C4 C5 C (2) C4 C5 C12 C (16) data-5

9 C3 C4 C5 C (13) C14 N1 C13 O (17) C2 C1 C6 C5 1.6 (2) C14 N1 C13 C (2) C8 C1 C6 C (13) O8 C12 C13 O (2) C4 C5 C6 C1 2.5 (2) C5 C12 C13 O (18) C12 C5 C6 C (13) C15 C12 C13 O (15) C6 C1 C8 O (19) O8 C12 C13 N (14) C2 C1 C8 O (12) C5 C12 C13 N (15) C6 C1 C8 C (15) C15 C12 C13 N (19) C2 C1 C8 C (17) C15 N2 C14 O (17) C6 C1 C8 C (15) C15 N2 C14 N1 8.6 (2) C2 C1 C8 C (17) C13 N1 C14 O (17) C10 N3 C9 O (18) C13 N1 C14 N2 0.7 (3) C10 N3 C9 C (2) C14 N2 C15 O (16) O4 C8 C9 O (2) C14 N2 C15 C (2) C1 C8 C9 O (2) O8 C12 C15 O (18) C11 C8 C9 O (17) C5 C12 C15 O (17) O4 C8 C9 N (16) C13 C12 C15 O (14) C1 C8 C9 N (14) O8 C12 C15 N (13) C11 C8 C9 N (19) C5 C12 C15 N (14) C9 N3 C10 O (16) C13 C12 C15 N (18) Hydrogen-bond geometry (Å, º) D H A D H H A D A D H A O1 H1O O1W i 0.81 (3) 1.97 (2) (18) 148 (2) O3 H3O O (3) 2.41 (2) (16) 112 (2) O3 H3O O2W ii 0.75 (3) 2.12 (3) (18) 147 (2) O4 H4O O9 iii 0.83 (2) 1.93 (2) (16) 168 (2) O8 H8O O6 iv 0.87 (3) 2.13 (2) (16) 140 (2) O8 H8O O4W v 0.87 (3) 2.63 (3) (19) 129 (2) N1 H1N O2W 0.92 (2) 1.97 (2) (19) 169 (2) N2 H2N O1W vi 0.89 (2) 1.92 (2) (18) (18) N3 H3N O3W vii 0.82 (3) 2.00 (3) (19) 167 (2) N4 H4N O4W vii 0.82 (2) 2.13 (2) (19) 158 (2) O1W H11W O10 ii 0.87 (2) 1.97 (2) (18) 161 (3) O1W H21W O5W 0.90 (2) 1.77 (2) (3) 164 (2) O2W H12W O5 viii 0.85 (2) 2.23 (2) (19) 165 (3) O2W H22W O4W 0.84 (2) 1.98 (2) (2) 175 (3) O3W H13W O7 vi 0.86 (2) 2.30 (2) (18) 147 (3) O3W H13W O (2) 2.44 (2) (19) 126 (3) O3W H23W O4 ix 0.83 (2) 2.10 (2) (18) 178 (3) O4W H14W O3W v 0.84 (2) 1.97 (2) (2) 178 (3) O4W H24W O11 viii 0.83 (2) 2.08 (2) (18) 168 (3) O5W H15W O (3) 164 O5W H25W O (3) 139 C7 H7B O7 i (2) 151 data-6

10 C7 H7B O11 x (2) 125 C7 H7C O10 ii (2) 159 Symmetry codes: (i) x, y, z+1; (ii) x+1, y+1, z+1; (iii) x, y, z; (iv) x+1, y+1, z; (v) x+1, y+1, z; (vi) x, y+1, z; (vii) x 1, y 1, z; (viii) x+1, y, z; (ix) x, y+1, z; (x) x, y+1, z+1. data-7