organic compounds
Benzoic acid–3,4-bis[(pyridin-3-ylmethyl)amino]cyclobut-3-ene-1,2-dione (1/2)
aMolecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, PO Wits 2050, South Africa, and bCentre for Supramolecular Chemistry Research, Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
*Correspondence e-mail: andreas.lemmerer@wits.ac.za
In the title 16H14N4O2·2C7H6O2, the 3,4-bis[(pyridin-3-ylmethyl)amino]cyclobut-3-ene-1,2-dione squareamide molecules assemble into chains along the b axis via N—H⋯O hydrogen bonds. The benzoic acid molecules then hydrogen bond to the pyridine rings via O—H⋯N hydrogen bonds, supported by weaker C—H⋯O hydrogen bonds, forming extended ribbons. The consists of a half squareamide molecule, sitting on a special position around a twofold axis, and one benzoic acid molecule on a general position.
CRelated literature
For the synthesis of related squareamides and co-crystals, see: Liu et al. (2002).
Experimental
Crystal data
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Refinement
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Data collection: COLLECT (Nonius, 2000); cell DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and DIAMOND (Brandenburg, 1999); software used to prepare material for publication: WinGX (Farrugia, 1999) and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536812000220/fy2039sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812000220/fy2039Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812000220/fy2039Isup3.mol
The title squareamide compound was synthesized according to literature procedures (Liu et al., 2002) by double condensation of diethyl squarate with 1-(pyridin-3-yl)methanamine in ethanol by stirring for 12 h. The resulting solid was filtered and dried. The squareamide was then dissolved in a 1:2 stoichiometric ratio with benzoic acid in a 1/1 v/v mixture of methanol and water. Plate-like, colourless crystals were harvested after a few days by slow evaporation at ambient conditions.
The C-bound H atoms were geometrically placed with C—H bond lengths of 0.95 Å (aromatic CH) and 0.99 Å (methylene CH2) and were refined as riding with Uiso(H) = 1.2Ueq(C). The N-bound and O-bound H atoms were located in the difference map and their coordinates and isotropic displacement parameters were refined freely.
Data collection: COLLECT (Nonius, 2000); cell
DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and DIAMOND (Brandenburg, 1999); software used to prepare material for publication: WinGX (Farrugia, 1999) and PLATON (Spek, 2009).C16H14N4O2·2C7H6O2 | F(000) = 1128 |
Mr = 538.55 | Dx = 1.356 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 16004 reflections |
a = 24.617 (5) Å | θ = 0.2–28.3° |
b = 6.0285 (12) Å | µ = 0.10 mm−1 |
c = 17.806 (4) Å | T = 173 K |
β = 93.08 (3)° | Plate, colourless |
V = 2638.6 (9) Å3 | 0.49 × 0.16 × 0.14 mm |
Z = 4 |
Nonius KappaCCD area-detector diffractometer | 2110 reflections with I > 2σ(I) |
2.0° ω scans | Rint = 0.076 |
Absorption correction: integration (XPREP; Bruker, 2004) | θmax = 28.0°, θmin = 2.3° |
Tmin = 0.944, Tmax = 0.989 | h = −32→26 |
15016 measured reflections | k = −7→7 |
3166 independent reflections | l = −23→21 |
Refinement on F2 | H atoms treated by a mixture of independent and constrained refinement |
Least-squares matrix: full | w = 1/[σ2(Fo2) + (0.0659P)2 + ] where P = (Fo2 + 2Fc2)/3 |
R[F2 > 2σ(F2)] = 0.044 | (Δ/σ)max < 0.001 |
wR(F2) = 0.116 | Δρmax = 0.23 e Å−3 |
S = 0.99 | Δρmin = −0.24 e Å−3 |
3166 reflections | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
190 parameters | Extinction coefficient: 0.0097 (11) |
0 restraints |
C16H14N4O2·2C7H6O2 | V = 2638.6 (9) Å3 |
Mr = 538.55 | Z = 4 |
Monoclinic, C2/c | Mo Kα radiation |
a = 24.617 (5) Å | µ = 0.10 mm−1 |
b = 6.0285 (12) Å | T = 173 K |
c = 17.806 (4) Å | 0.49 × 0.16 × 0.14 mm |
β = 93.08 (3)° |
Nonius KappaCCD area-detector diffractometer | 3166 independent reflections |
Absorption correction: integration (XPREP; Bruker, 2004) | 2110 reflections with I > 2σ(I) |
Tmin = 0.944, Tmax = 0.989 | Rint = 0.076 |
15016 measured reflections |
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.116 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.99 | Δρmax = 0.23 e Å−3 |
3166 reflections | Δρmin = −0.24 e Å−3 |
190 parameters |
Experimental. Numerical integration absorption corrections based on indexed crystal faces were applied using the XPREP routine (Bruker, 2004). |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.09548 (5) | 0.7538 (2) | 0.57965 (7) | 0.0286 (3) | |
C2 | 0.10973 (5) | 0.5561 (2) | 0.54679 (7) | 0.0333 (3) | |
H2A | 0.0814 | 0.4569 | 0.5308 | 0.04* | |
C3 | 0.20066 (6) | 0.6353 (3) | 0.55968 (8) | 0.0417 (4) | |
H3 | 0.2373 | 0.5946 | 0.5526 | 0.05* | |
C4 | 0.19060 (6) | 0.8346 (3) | 0.59354 (8) | 0.0430 (4) | |
H4 | 0.2198 | 0.929 | 0.61 | 0.052* | |
C5 | 0.13726 (6) | 0.8956 (2) | 0.60321 (7) | 0.0366 (3) | |
H5 | 0.1293 | 1.0337 | 0.6259 | 0.044* | |
C6 | 0.03667 (5) | 0.8124 (2) | 0.58837 (7) | 0.0307 (3) | |
H6A | 0.0312 | 0.9723 | 0.5777 | 0.037* | |
H6B | 0.0136 | 0.7275 | 0.5513 | 0.037* | |
C7 | 0.00897 (5) | 0.91990 (19) | 0.71280 (7) | 0.0261 (3) | |
C8 | 0.01001 (5) | 1.16213 (19) | 0.71131 (7) | 0.0293 (3) | |
N1 | 0.02002 (4) | 0.76350 (17) | 0.66414 (6) | 0.0298 (3) | |
H1 | 0.0195 (6) | 0.616 (3) | 0.6757 (8) | 0.041 (4)* | |
N2 | 0.16108 (5) | 0.49629 (19) | 0.53623 (6) | 0.0384 (3) | |
O1 | 0.02247 (4) | 1.30418 (13) | 0.66529 (5) | 0.0373 (3) | |
C9 | 0.14385 (5) | −0.1060 (2) | 0.36020 (7) | 0.0350 (3) | |
C10 | 0.18500 (6) | −0.0836 (2) | 0.31016 (8) | 0.0423 (4) | |
H10 | 0.208 | 0.0431 | 0.3128 | 0.051* | |
C11 | 0.19255 (7) | −0.2448 (3) | 0.25655 (9) | 0.0513 (4) | |
H11 | 0.2201 | −0.2273 | 0.2217 | 0.062* | |
C12 | 0.16006 (8) | −0.4312 (3) | 0.25359 (9) | 0.0573 (5) | |
H12 | 0.1657 | −0.543 | 0.2172 | 0.069* | |
C13 | 0.11934 (8) | −0.4557 (3) | 0.30324 (10) | 0.0559 (5) | |
H13 | 0.0972 | −0.5848 | 0.3013 | 0.067* | |
C14 | 0.11075 (6) | −0.2923 (3) | 0.35590 (8) | 0.0452 (4) | |
H14 | 0.0821 | −0.3078 | 0.3892 | 0.054* | |
C15 | 0.13450 (6) | 0.0665 (2) | 0.41783 (8) | 0.0374 (4) | |
O2 | 0.17883 (4) | 0.18069 (17) | 0.43789 (6) | 0.0443 (3) | |
H2 | 0.1708 (7) | 0.309 (3) | 0.4774 (11) | 0.080 (6)* | |
O3 | 0.09068 (4) | 0.09691 (18) | 0.44435 (6) | 0.0484 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0315 (7) | 0.0303 (7) | 0.0247 (6) | 0.0022 (5) | 0.0069 (5) | 0.0042 (5) |
C2 | 0.0308 (7) | 0.0342 (7) | 0.0355 (7) | 0.0025 (6) | 0.0083 (6) | −0.0004 (5) |
C3 | 0.0282 (8) | 0.0576 (9) | 0.0400 (8) | 0.0050 (7) | 0.0092 (6) | 0.0049 (7) |
C4 | 0.0339 (8) | 0.0501 (9) | 0.0452 (8) | −0.0078 (7) | 0.0033 (6) | 0.0024 (7) |
C5 | 0.0401 (8) | 0.0324 (7) | 0.0376 (8) | −0.0007 (6) | 0.0065 (6) | 0.0003 (6) |
C6 | 0.0320 (7) | 0.0289 (7) | 0.0319 (7) | 0.0048 (5) | 0.0081 (5) | 0.0008 (5) |
C7 | 0.0227 (6) | 0.0211 (6) | 0.0353 (7) | 0.0006 (5) | 0.0073 (5) | 0.0000 (5) |
C8 | 0.0282 (7) | 0.0219 (6) | 0.0384 (7) | 0.0012 (5) | 0.0084 (5) | 0.0004 (5) |
N1 | 0.0355 (6) | 0.0203 (6) | 0.0348 (6) | 0.0017 (5) | 0.0130 (5) | 0.0013 (4) |
N2 | 0.0335 (7) | 0.0443 (7) | 0.0384 (7) | 0.0092 (5) | 0.0103 (5) | −0.0012 (5) |
O1 | 0.0468 (6) | 0.0225 (5) | 0.0440 (5) | −0.0014 (4) | 0.0159 (4) | 0.0046 (4) |
C9 | 0.0308 (7) | 0.0419 (8) | 0.0324 (7) | 0.0077 (6) | 0.0018 (6) | 0.0064 (6) |
C10 | 0.0372 (8) | 0.0459 (8) | 0.0445 (9) | 0.0044 (6) | 0.0093 (7) | 0.0008 (6) |
C11 | 0.0507 (10) | 0.0624 (11) | 0.0417 (9) | 0.0148 (8) | 0.0099 (7) | −0.0028 (8) |
C12 | 0.0702 (12) | 0.0560 (11) | 0.0441 (9) | 0.0146 (9) | −0.0110 (9) | −0.0100 (7) |
C13 | 0.0640 (12) | 0.0507 (10) | 0.0510 (10) | −0.0084 (8) | −0.0155 (9) | −0.0003 (8) |
C14 | 0.0393 (9) | 0.0593 (10) | 0.0367 (8) | −0.0032 (7) | −0.0025 (6) | 0.0077 (7) |
C15 | 0.0310 (8) | 0.0460 (9) | 0.0356 (8) | 0.0100 (6) | 0.0066 (6) | 0.0074 (6) |
O2 | 0.0331 (6) | 0.0490 (6) | 0.0518 (6) | 0.0063 (5) | 0.0112 (5) | −0.0115 (5) |
O3 | 0.0322 (6) | 0.0669 (7) | 0.0472 (6) | 0.0120 (5) | 0.0133 (5) | 0.0027 (5) |
C1—C2 | 1.3816 (18) | C8—C8i | 1.488 (3) |
C1—C5 | 1.3849 (19) | N1—H1 | 0.915 (16) |
C1—C6 | 1.5061 (18) | C9—C14 | 1.387 (2) |
C2—N2 | 1.3374 (17) | C9—C10 | 1.391 (2) |
C2—H2A | 0.95 | C9—C15 | 1.487 (2) |
C3—N2 | 1.3351 (19) | C10—C11 | 1.382 (2) |
C3—C4 | 1.373 (2) | C10—H10 | 0.95 |
C3—H3 | 0.95 | C11—C12 | 1.378 (2) |
C4—C5 | 1.383 (2) | C11—H11 | 0.95 |
C4—H4 | 0.95 | C12—C13 | 1.380 (3) |
C5—H5 | 0.95 | C12—H12 | 0.95 |
C6—N1 | 1.4612 (16) | C13—C14 | 1.384 (2) |
C6—H6A | 0.99 | C13—H13 | 0.95 |
C6—H6B | 0.99 | C14—H14 | 0.95 |
C7—N1 | 1.3187 (16) | C15—O3 | 1.2146 (16) |
C7—C7i | 1.419 (2) | C15—O2 | 1.3231 (17) |
C7—C8 | 1.4607 (17) | O2—H2 | 1.07 (2) |
C8—O1 | 1.2354 (15) | ||
C2—C1—C5 | 117.35 (12) | C7—N1—C6 | 122.71 (11) |
C2—C1—C6 | 120.89 (12) | C7—N1—H1 | 122.9 (9) |
C5—C1—C6 | 121.76 (12) | C6—N1—H1 | 114.3 (9) |
N2—C2—C1 | 123.74 (13) | C3—N2—C2 | 117.80 (12) |
N2—C2—H2A | 118.1 | C14—C9—C10 | 119.28 (14) |
C1—C2—H2A | 118.1 | C14—C9—C15 | 119.46 (13) |
N2—C3—C4 | 122.74 (13) | C10—C9—C15 | 121.26 (13) |
N2—C3—H3 | 118.6 | C11—C10—C9 | 120.24 (15) |
C4—C3—H3 | 118.6 | C11—C10—H10 | 119.9 |
C3—C4—C5 | 118.83 (14) | C9—C10—H10 | 119.9 |
C3—C4—H4 | 120.6 | C12—C11—C10 | 120.03 (16) |
C5—C4—H4 | 120.6 | C12—C11—H11 | 120 |
C4—C5—C1 | 119.53 (13) | C10—C11—H11 | 120 |
C4—C5—H5 | 120.2 | C11—C12—C13 | 120.19 (15) |
C1—C5—H5 | 120.2 | C11—C12—H12 | 119.9 |
N1—C6—C1 | 111.52 (10) | C13—C12—H12 | 119.9 |
N1—C6—H6A | 109.3 | C12—C13—C14 | 120.03 (16) |
C1—C6—H6A | 109.3 | C12—C13—H13 | 120 |
N1—C6—H6B | 109.3 | C14—C13—H13 | 120 |
C1—C6—H6B | 109.3 | C13—C14—C9 | 120.20 (16) |
H6A—C6—H6B | 108 | C13—C14—H14 | 119.9 |
N1—C7—C7i | 134.35 (7) | C9—C14—H14 | 119.9 |
N1—C7—C8 | 134.30 (12) | O3—C15—O2 | 123.58 (13) |
C7i—C7—C8 | 91.35 (7) | O3—C15—C9 | 123.19 (14) |
O1—C8—C7 | 135.25 (12) | O2—C15—C9 | 113.22 (12) |
O1—C8—C8i | 136.11 (7) | C15—O2—H2 | 111.9 (10) |
C7—C8—C8i | 88.64 (7) | ||
C5—C1—C2—N2 | −0.52 (19) | C4—C3—N2—C2 | −0.2 (2) |
C6—C1—C2—N2 | 178.76 (11) | C1—C2—N2—C3 | 0.8 (2) |
N2—C3—C4—C5 | −0.7 (2) | C14—C9—C10—C11 | 0.3 (2) |
C3—C4—C5—C1 | 0.9 (2) | C15—C9—C10—C11 | −179.30 (13) |
C2—C1—C5—C4 | −0.35 (19) | C9—C10—C11—C12 | −1.5 (2) |
C6—C1—C5—C4 | −179.62 (12) | C10—C11—C12—C13 | 1.1 (2) |
C2—C1—C6—N1 | 98.57 (14) | C11—C12—C13—C14 | 0.5 (2) |
C5—C1—C6—N1 | −82.19 (14) | C12—C13—C14—C9 | −1.6 (2) |
N1—C7—C8—O1 | −1.8 (3) | C10—C9—C14—C13 | 1.2 (2) |
C7i—C7—C8—O1 | 178.55 (15) | C15—C9—C14—C13 | −179.17 (13) |
N1—C7—C8—C8i | 178.45 (15) | C14—C9—C15—O3 | −25.7 (2) |
C7i—C7—C8—C8i | −1.20 (14) | C10—C9—C15—O3 | 153.96 (14) |
C7i—C7—N1—C6 | 178.04 (17) | C14—C9—C15—O2 | 153.46 (12) |
C8—C7—N1—C6 | −1.5 (2) | C10—C9—C15—O2 | −26.92 (18) |
C1—C6—N1—C7 | 110.22 (13) |
Symmetry code: (i) −x, y, −z+3/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1ii | 0.915 (16) | 1.889 (17) | 2.7697 (15) | 161.0 (13) |
O2—H2···N2 | 1.07 (2) | 1.57 (2) | 2.6380 (15) | 178.0 (17) |
C2—H2A···O3 | 0.95 | 2.68 | 3.3341 (18) | 127 |
Symmetry code: (ii) x, y−1, z. |
Experimental details
Crystal data | |
Chemical formula | C16H14N4O2·2C7H6O2 |
Mr | 538.55 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 173 |
a, b, c (Å) | 24.617 (5), 6.0285 (12), 17.806 (4) |
β (°) | 93.08 (3) |
V (Å3) | 2638.6 (9) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.49 × 0.16 × 0.14 |
Data collection | |
Diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | Integration (XPREP; Bruker, 2004) |
Tmin, Tmax | 0.944, 0.989 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 15016, 3166, 2110 |
Rint | 0.076 |
(sin θ/λ)max (Å−1) | 0.660 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.116, 0.99 |
No. of reflections | 3166 |
No. of parameters | 190 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.23, −0.24 |
Computer programs: COLLECT (Nonius, 2000), DENZO-SMN (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and DIAMOND (Brandenburg, 1999), WinGX (Farrugia, 1999) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.915 (16) | 1.889 (17) | 2.7697 (15) | 161.0 (13) |
O2—H2···N2 | 1.07 (2) | 1.57 (2) | 2.6380 (15) | 178.0 (17) |
C2—H2A···O3 | 0.95 | 2.68 | 3.3341 (18) | 127 |
Symmetry code: (i) x, y−1, z. |
Acknowledgements
This work was supported by the University of the Witwatersrand, which is thanked for providing the infrastructure required to do this work.
References
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The title compound is a further example of co-crystals formed by squareamide molecules, in this case 3,4-bis[(pyridin-3-ylmethyl)amino]cyclobut-3-ene-1,2-dione, with carboxylic acid containing co-former molecules. Related co-crystals where the squaureamide molecule has the pyridine N atom in the 4 position are reported by Liu et al. (2002). The asymmetric unit consists of one half squareamide molecule, sitting around a twofold axis, and one complete benzoic acid molecule, on a general position (Fig. 1). The squareamide self-assembles into chains using the two N—H···O hydrogen bonds formed from the two amine N—-H groups to the diketones. The pyridine rings then act as hydrogen bond acceptors to the carboxylic acid functional group of the two benzoic acid molecules (Fig. 2).