data reports cis-cyclohexane-1,3-dicarboxylic acid N,N 0 -(pentane-1,5-diyl)bis(pyridine-4-carboxamide) water (1/1/2) Structure description

Transcription

1 ISSN cis-cyclohexane-1,3-dicarboxylic acid N,N 0 -(pentane-1,5-diyl)bis(pyridine-4-carboxamide) water (1/1/2) Brianna L. Martinez and Robert L. LaDuca* Received 23 September 2017 Accepted 12 October 2017 Edited by A. J. Lough, University of Toronto, Canada Keywords: crystal structure; cocrystal; hydrogen bonding. CCDC reference: E-35 Holmes Hall, Lyman Briggs College, Michigan State University, 919 E. Shaw Lane, East Lansing, MI 48825, USA. *Correspondence laduca@msu.edu The title cocrystal, C 8 H 12 O 4 C 17 H 20 N 4 O 2 2H 2 O, shows O HN hydrogen bonded supramolecular chain motifs of cis-1,3-cyclohexanedicarboxylic acid (H 2 cdc) molecules alternating with N,N 0 -(pentane-1,5-diyl)bis(pyridine-4- carboxamide)pentane (bpcpe) molecules. These chain motifs are aggregated by C HO interactions into supramolecular layers and slabs, which are stacked into the three-dimensional crystal structure by means of O HO interactions mediated by the water molecules of crystallization. Structural data: full structural data are available from iucrdata.iucr.org Structure description The title compound was isolated during an exploratory synthetic effort aiming to produce divalent cadmium coordination polymers containing both cis-cyclohexane-1,3-dicarboxylate (cdc) and N,N 0 -(pentane-1,5-diyl)bis(pyridine-4-carboxamide) (bpcpe) ligands. Reports of cadmium coordination polymers containing cdc ligands have been seldom to date, with {[Cd(L)(cdc)]H 2 O} n [L = 1,3-di(1H-imidazol-4-yl)benzene] representing one of the few known examples (Chen et al., 2014). The bpcpe ligand has also rarely been used in coordination polymer chemistry to this point, with {[Cu(bpcpe) 2 - (H 2 O) 2 )(ClO 4 ) 2 ]2H 2 O4CH 3 OH} n being one of the very few reported examples (Mukherjee & Biradha, 2013). The asymmetric unit of the title cocrystal contains a cis-cyclohexane-1,3-dicarboxylic acid (H 2 cdc) molecule, a bpcpe molecule, and two water molecules of crystallization (Fig. 1). Adjacent H 2 cdc and bpcpe molecules form supramolecular chain motifs (Fig. 2) by means of O HN hydrogen-bonding interactions (Table 1) between protonated H 2 cdc carboxylate groups and the pyridyl ring N atoms in the bpcpe molecules. Nonclassical C HO interactions (C9 H9O2 iv and C21 H21O4 v ; Table 1) between bpcpe pyridyl rings and unprotonated H 2 cdc O atoms construct supramolecular layer motifs oriented parallel to the ab crystal planes (Fig. 3). Additional C HO 1of3

2 Table 1 Hydrogen-bond geometry (Å, ). D HA D H HA DA D HA O1 H1N (18) 178 O3 H3AN4 i (19) 173 N2 H2O1W ii (19) 165 N3 H3O2W ii (2) 159 O2W H2WAO2 iii (2) 177 O2W H2WBO (19) 173 O1W H1WAO (18) 168 O1W H1WBO4 iii (2) 178 C9 H9O2 iv (2) 124 C21 H21O4 v (2) 139 C6 H6O6 vi (2) 167 Symmetry codes: (i) x; y þ 1; z; (ii) x þ 1; y; z; (iii) x þ 1; y 1 2 ; z þ 3 2 ; (iv) x 1; y; z; (v) x 1; y 1; z; (vi) x þ 1; y þ 1; z þ 1. Table 2 Experimental details. Crystal data Chemical formula C 8 H 12 O 4 C 17 H 20 N 4 O 2 2H 2 O M r Crystal system, space group Monoclinic, P2 1 /c Temperature (K) 173 a, b, c (Å) (9), (3), (19) ( ) (2) V (Å 3 ) (6) Z 4 Radiation type Mo K (mm 1 ) 0.10 Crystal size (mm) Data collection Diffractometer Bruker APEXII CCD Absorption correction Multi-scan (SADABS; Bruker, 2014) T min, T max 0.677, No. of measured, independent and 21494, 4904, 3656 observed [I > 2(I)] reflections R int (sin /) max (Å 1 ) Refinement R[F 2 >2(F 2 )], wr(f 2 ), S 0.046, 0.136, 1.04 No. of reflections 4904 No. of parameters 342 H-atom treatment H-atom parameters constrained max, min (e Å 3 ) 0.23, 0.22 Figure 1 The asymmetric unit of the title cocrystal. Displacement ellipsoids are drawn at the 50% probability level. The H-atom positions are denoted by gray sticks. Color code: N blue, O red, C black, and H grey. Computer programs: COSMO (Bruker, 2009), APEX2 (Bruker, 2012), SAINT (Bruker, 2013), SHELXS97 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), CrystalMaker (Palmer, 2013) and OLEX2 (Dolomanov et al., 2009). interactions (C6 H6O6 vi ; Table 1) between the tertiary C atoms of the H 2 cdc molecules and bpcpe C O carbonyl O atoms result in bilayer slab motifs (Fig. 4). Supramolecular O HO hydrogen-bonding interactions (Table 1) mediated by the water molecules of crystallization aggregate the supramolecular slabs into the full three-dimensional crystal structure of the title cocrystal (Fig. 5). Synthesis and crystallization Cd(NO 3 ) 2 4H 2 O (114 mg, 0.37 mmol), cis-cyclohexane-1,3-dicarboxylic acid (64 mg, 0.37 mmol), bpcpe (115 mg, 0.37 mmol) and 0.75 ml of a 1.0 M NaOH solution were placed into 10 ml distilled H 2 O in a Teflon-lined acid digestion bomb. The bomb was sealed and heated in an oven at 393 K for 2 d, and then cooled slowly to 273 K. Colorless crystals of the title cocrystal (74 mg, 38% yield, based on cis-cyclohexane-1,3-dicarboxylic acid) were isolated after washing with distilled water and acetone, and drying in air. Figure 3 Supramolecular layer motif parallel to the ab crystal planes formed by nonclassical C HO interactions (shown as dashed lines) between neighboring chain motifs. Refinement Crystal data, data collection and structure refinement details are summarized in Table 2. Figure 2 A hydrogen-bonded chain in the title cocrystal, oriented parallel to [010]. O HN hydrogen bonds are shown as dashed lines. 2of3 Martinez and LaDuca C 8 H 12 O 4 C 17 H 20 N 4 O 2 2H 2 O

3 Figure 4 Aggregation of supramolecular layers into bilayer slabs by additional. C HO hydrogen-bonding interactions (shown as dashed lines). Figure 5 Stacking of supramolecular slab motifs in the title cocrystal, to afford the three-dimensional crystal structure, mediated by O HO hydrogen-bonding interactions (shown as dashed lines) involving the water molecules of crystallization. Acknowledgements We thank Dr Richard Staples for crystallographic assistance. Funding information Funding for this research was provided by: Michigan State University Honors College. References Bruker (2009). COSMO. Bruker AXS Inc., Madison, Wisconsin, USA. Bruker (2012). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA. Bruker (2013). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Bruker (2014). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Chen, Z., Zhao, Y., Wang, P., Chen, S. S. & Sun, W. Y. (2014). Polyhedron, 67, Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, Mukherjee, G. & Biradha, K. (2013). Cryst. Growth Des. 13, Palmer, D. (2013). CrystalMaker. CrystalMaker Software, Bicester, Oxfordshire, England. Sheldrick, G. M. (2008). Acta Cryst. A64, Sheldrick, G. M. (2015). Acta Cryst. A71, 3 8. Martinez and LaDuca C 8 H 12 O 4 C 17 H 20 N 4 O 2 2H 2 O 3of3

4 full crystallographic data [ cis-cyclohexane-1,3-dicarboxylic acid N,N -(pentane-1,5-diyl)bis(pyridine-4- carboxamide) water (1/1/2) Brianna L. Martinez and Robert L. LaDuca cis-cyclohexane-1,3-dicarboxylic acid N,N -(pentane-1,5-diyl)bis(pyridine-4-carboxamide) water (1/1/2) Crystal data C 8 H 12 O 4 C 17 H 20 N 4 O 2 2H 2 O M r = Monoclinic, P2 1 /c a = (9) Å b = (3) Å c = (19) Å β = (2) V = (6) Å 3 Z = 4 Data collection Bruker APEXII CCD diffractometer Radiation source: sealed tube Graphite monochromator Detector resolution: 8.4 pixels mm -1 φ and ω scans Absorption correction: multi-scan (SADABS; Bruker, 2014) T min = 0.677, T max = Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = S = reflections 342 parameters 0 restraints F(000) = 1112 D x = Mg m 3 Mo Kα radiation, λ = Å Cell parameters from 7916 reflections θ = µ = 0.10 mm 1 T = 173 K Chunk, yellow mm measured reflections 4904 independent reflections 3656 reflections with I > 2σ(I) R int = θ max = 25.4, θ min = 1.6 h = 8 8 k = l = Primary atom site location: dual Hydrogen site location: mixed H-atom parameters constrained w = 1/[σ 2 (F o2 ) + (0.0742P) P] where P = (F o 2 + 2F c2 )/3 (Δ/σ) max < Δρ max = 0.23 e Å 3 Δρ min = 0.22 e Å 3 data-1

5 Special details Experimental. Data was collected using a BRUKER CCD (charge coupled device) based diffractometer equipped with an Oxford low-temperature apparatus operating at 173 K. A suitable crystal was chosen and mounted on a nylon loop using Paratone oil. Data were measured using omega and phi scans of 0.5 per frame for 30 s. The total number of images were based on results from the program COSMO where redundancy was expected to be 4 and completeness to 0.83Å to 100%. Cell parameters were retrieved using APEX II software and refined using SAINT on all observed reflections.data reduction was performed using the SAINT software which corrects for Lp. Scaling and absorption corrections were applied using SADABS6 multi-scan technique, supplied by George Sheldrick. The structures are solved by the direct method using the SHELXS-97 program and refined by least squares method on F2, SHELXL-97, incorporated in OLEX2. 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. 1. Fixed Uiso At 1.2 times of: All C(H) groups, All C(H,H) groups, All N(H) groups At 1.5 times of: All O(H) groups, All O(H,H) groups 2.a Free rotating group: O2W(H2WA,H2WB), O1W(H1WA,H1WB) 2.b Ternary CH refined with riding coordinates: C2(H2A), C6(H6) 2.c Secondary CH2 refined with riding coordinates: C1(H1A,H1B), C3(H3B,H3C), C4(H4A,H4B), C5(H5A,H5B), C15(H15A,H15B), C16(H16A, H16B), C17(H17A,H17B), C18(H18A,H18B), C19(H19A,H19B) 2.d Aromatic/amide H refined with riding coordinates: N2(H2), N3(H3), C9(H9), C10(H10), C12(H12), C13(H13), C21(H21), C22(H22), C24(H24), C25(H25) 2.e Idealised tetrahedral OH refined as rotating group: O1(H1), O3(H3A) Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 ) x y z U iso */U eq O (18) (5) (9) (3) H * O (19) (5) (11) (4) O (19) (5) (10) (4) H3A * O (2) (6) (10) (5) O (17) (5) (9) (3) O (17) (5) (9) (3) N (2) (5) (9) (3) N (2) (5) (9) (3) H * N (2) (5) (9) (3) H * N (2) (5) (10) (4) C (2) (6) (11) (4) H1A * H1B * C (2) (6) (11) (4) H2A * C (3) (7) (13) (4) H3B * H3C * C (3) (7) (13) (5) H4A * H4B * data-2

6 C (3) (7) (13) (4) H5A * H5B * C (2) (6) (12) (4) H * C (3) (6) (11) (4) C (3) (7) (12) (4) C (3) (7) (12) (4) H * C (3) (7) (12) (4) H * C (2) (6) (10) (4) C (2) (6) (11) (4) H * C (3) (6) (11) (4) H * C (2) (6) (11) (4) C (2) (6) (12) (4) H15A * H15B * C (3) (6) (12) (4) H16A * H16B * C (3) (6) (12) (4) H17A * H17B * C (3) (6) (12) (4) H18A * H18B * C (3) (6) (12) (4) H19A * H19B * C (2) (6) (11) (4) C (3) (7) (13) (5) H * C (3) (7) (12) (4) H * C (2) (6) (11) (4) C (3) (6) (12) (4) H * C (3) (7) (13) (4) H * O2W (19) (6) (11) (4) H2WA * H2WB * O1W (18) (6) (10) (4) H1WA * H1WB * data-3

7 Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 O (7) (7) (8) (5) (6) (6) O (8) (7) (11) (6) (7) (7) O (8) (8) (9) (6) (7) (7) O (9) (10) (11) (8) (8) (8) O (7) (7) (8) (5) (6) (6) O (7) (8) (8) (6) (6) (6) N (9) (7) (8) (6) (6) (6) N (7) (7) (8) (6) (6) (6) N (8) (7) (9) (6) (6) (6) N (10) (8) (9) (7) (7) (7) C (9) (9) (10) (7) (7) (7) C (9) (8) (9) (7) (7) (7) C (10) (9) (12) (8) (9) (8) C (10) (10) (12) (8) (9) (9) C (10) (10) (11) (8) (8) (8) C (9) (9) (9) (7) (7) (7) C (10) (9) (9) (7) (7) (7) C (11) (9) (10) (8) (8) (8) C (10) (9) (11) (8) (8) (8) C (9) (9) (10) (7) (8) (8) C (9) (8) (9) (7) (7) (7) C (9) (9) (9) (7) (7) (7) C (9) (9) (10) (7) (8) (7) C (9) (9) (9) (7) (7) (7) C (9) (8) (10) (7) (8) (7) C (10) (9) (10) (7) (8) (7) C (10) (9) (10) (7) (8) (7) C (9) (9) (10) (7) (8) (7) C (10) (9) (11) (7) (8) (8) C (10) (9) (9) (7) (7) (7) C (12) (10) (12) (8) (9) (8) C (10) (10) (11) (8) (8) (8) C (9) (8) (9) (7) (7) (7) C (10) (9) (11) (7) (8) (8) C (10) (9) (12) (8) (9) (9) O2W (7) (9) (11) (7) (7) (9) O1W (7) (10) (10) (7) (7) (8) Geometric parameters (Å, º) O1 H C9 H O1 C (2) C9 C (2) O2 C (2) C10 H O3 H3A C10 C (2) O3 C (2) C11 C (2) data-4

8 O4 C (2) C11 C (2) O5 C (2) C12 H O6 C (2) C12 C (2) N1 C (2) C13 H N1 C (2) C15 H15A N2 H C15 H15B N2 C (2) C15 C (2) N2 C (2) C16 H16A N3 H C16 H16B N3 C (2) C16 C (2) N3 C (2) C17 H17A N4 C (2) C17 H17B N4 C (2) C17 C (2) C1 H1A C18 H18A C1 H1B C18 H18B C1 C (2) C18 C (2) C1 C (2) C19 H19A C2 H2A C19 H19B C2 C (2) C20 C (2) C2 C (2) C21 H C3 H3B C21 C (3) C3 H3C C22 H C3 C (2) C22 C (2) C4 H4A C23 C (2) C4 H4B C24 H C4 C (3) C24 C (2) C5 H5A C25 H C5 H5B O2W H2WA C5 C (2) O2W H2WB C6 H O1W H1WA C6 C (2) O1W H1WB C7 O1 H C12 C11 C (14) C8 O3 H3A C11 C12 H C9 N1 C (14) C13 C12 C (15) C14 N2 H C13 C12 H C14 N2 C (14) N1 C13 C (16) C15 N2 H N1 C13 H C19 N3 H C12 C13 H C20 N3 H O5 C14 N (15) C20 N3 C (15) O5 C14 C (15) C21 N4 C (15) N2 C14 C (14) H1A C1 H1B N2 C15 H15A C2 C1 H1A N2 C15 H15B C2 C1 H1B N2 C15 C (14) C2 C1 C (14) H15A C15 H15B C6 C1 H1A C16 C15 H15A C6 C1 H1B C16 C15 H15B data-5

9 C1 C2 H2A C15 C16 H16A C3 C2 C (14) C15 C16 H16B C3 C2 H2A C15 C16 C (14) C7 C2 C (13) H16A C16 H16B C7 C2 H2A C17 C16 H16A C7 C2 C (14) C17 C16 H16B C2 C3 H3B C16 C17 H17A C2 C3 H3C C16 C17 H17B H3B C3 H3C H17A C17 H17B C4 C3 C (14) C18 C17 C (14) C4 C3 H3B C18 C17 H17A C4 C3 H3C C18 C17 H17B C3 C4 H4A C17 C18 H18A C3 C4 H4B C17 C18 H18B C3 C4 C (15) H18A C18 H18B H4A C4 H4B C19 C18 C (14) C5 C4 H4A C19 C18 H18A C5 C4 H4B C19 C18 H18B C4 C5 H5A N3 C19 C (14) C4 C5 H5B N3 C19 H19A H5A C5 H5B N3 C19 H19B C6 C5 C (15) C18 C19 H19A C6 C5 H5A C18 C19 H19B C6 C5 H5B H19A C19 H19B C1 C6 H O6 C20 N (15) C5 C6 C (14) O6 C20 C (15) C5 C6 H N3 C20 C (14) C8 C6 C (14) N4 C21 H C8 C6 C (14) N4 C21 C (17) C8 C6 H C22 C21 H O1 C7 C (14) C21 C22 H O2 C7 O (16) C23 C22 C (17) O2 C7 C (16) C23 C22 H O3 C8 C (15) C22 C23 C (15) O4 C8 O (17) C22 C23 C (15) O4 C8 C (17) C24 C23 C (15) N1 C9 H C23 C24 H N1 C9 C (16) C25 C24 C (17) C10 C9 H C25 C24 H C9 C10 H N4 C25 C (17) C9 C10 C (16) N4 C25 H C11 C10 H C24 C25 H C10 C11 C (14) H2WA O2W H2WB C12 C11 C (15) H1WA O1W H1WB O6 C20 C23 C (2) C9 C10 C11 C (2) O6 C20 C23 C (16) C9 C10 C11 C (15) N1 C9 C10 C (3) C10 C11 C12 C (2) data-6

10 N2 C15 C16 C (14) C10 C11 C14 O5 6.9 (2) N3 C20 C23 C (15) C10 C11 C14 N (15) N3 C20 C23 C (2) C11 C12 C13 N1 0.1 (3) N4 C21 C22 C (3) C12 C11 C14 O (16) C1 C2 C3 C (2) C12 C11 C14 N2 6.4 (2) C1 C2 C7 O (19) C13 N1 C9 C (3) C1 C2 C7 O (19) C14 N2 C15 C (15) C1 C6 C8 O (2) C14 C11 C12 C (15) C1 C6 C8 O (2) C15 N2 C14 O5 2.1 (2) C2 C1 C6 C (19) C15 N2 C14 C (14) C2 C1 C6 C (14) C15 C16 C17 C (16) C2 C3 C4 C (2) C16 C17 C18 C (15) C3 C2 C7 O (15) C17 C18 C19 N (15) C3 C2 C7 O (2) C19 N3 C20 O6 4.5 (3) C3 C4 C5 C (2) C19 N3 C20 C (14) C4 C5 C6 C (2) C20 N3 C19 C (17) C4 C5 C6 C (15) C20 C23 C24 C (16) C5 C6 C8 O (15) C21 N4 C25 C (3) C5 C6 C8 O4 3.5 (3) C21 C22 C23 C (16) C6 C1 C2 C (18) C21 C22 C23 C (3) C6 C1 C2 C (14) C22 C23 C24 C (3) C7 C2 C3 C (15) C23 C24 C25 N4 0.2 (3) C9 N1 C13 C (2) C25 N4 C21 C (3) Hydrogen-bond geometry (Å, º) D H A D H H A D A D H A O1 H1 N (18) 178 O3 H3A N4 i (19) 173 N2 H2 O1W ii (19) 165 N3 H3 O2W ii (2) 159 O2W H2WA O2 iii (2) 177 O2W H2WB O (19) 173 O1W H1WA O (18) 168 O1W H1WB O4 iii (2) 178 C9 H9 O2 iv (2) 124 C21 H21 O4 v (2) 139 C6 H6 O6 vi (2) 167 Symmetry codes: (i) x, y+1, z; (ii) x+1, y, z; (iii) x+1, y 1/2, z+3/2; (iv) x 1, y, z; (v) x 1, y 1, z; (vi) x+1, y+1, z+1. data-7