organic compounds
Bis(2,3-diaminopyridinium) phthalate dihydrate
aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
The complete anion of the title hydrated molecular salt, 2C5H8N3+·C8H4O4−·2H2O, is generated by a crystallographic twofold axis. In the crystal, the cations, anions and water molecules are connected by N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds, forming a three-dimensional network. The also features C—H⋯π interactions.
Related literature
For background to hydrogen-bonding patterns of 2-aminopyridine derivatives, see: Gellert & Hsu (1988); Banerjee & Murugavel (2004). For related structures, see: Hemamalini & Fun (2010a,b,c). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
10.1107/S1600536811055838/hb6574sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811055838/hb6574Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536811055838/hb6574Isup3.cml
A hot methanol solution (20 ml) of 2,3-diaminopyridine (27 mg, Aldrich) and phthalic acid (42 mg, Merck) were mixed and warmed over a magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and brown plates of the title compound appeared after a few days.
All hydrogen atoms were located from a difference Fourier maps and refined freely [N–H = 0.89 (2)–0.98 (2)Å; O–H = 0.91 (2)– 0.95 (3) Å and C–H = 0.959 (18)–1.01 (2) Å]. The highest residual electron density peak is located at 0.73 Å from C9 and the deepest hole is located at 0.78 Å from C9.
Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).Fig. 1. The molecule of (I) with 30% probability displacement ellipsoids. Atoms labelled A are generated by -x+1, y, -z+1/2. | |
Fig. 2. The crystal packing of the title compound showing hydrogen-bonded (dashed lines) networks. H atoms not involved in hydrogen bond interactions are omitted for clarity. |
2C5H8N3+·C8H4O4−·2H2O | F(000) = 888 |
Mr = 420.43 | Dx = 1.356 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 3390 reflections |
a = 15.795 (5) Å | θ = 2.8–29.8° |
b = 13.083 (4) Å | µ = 0.10 mm−1 |
c = 11.012 (4) Å | T = 100 K |
β = 115.194 (5)° | Plate, brown |
V = 2059.2 (11) Å3 | 0.42 × 0.36 × 0.03 mm |
Z = 4 |
Bruker APEXII DUO CCD diffractometer | 2955 independent reflections |
Radiation source: fine-focus sealed tube | 2148 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.042 |
ϕ and ω scans | θmax = 29.9°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −22→22 |
Tmin = 0.958, Tmax = 0.997 | k = −18→18 |
10343 measured reflections | l = −14→14 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.043 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.125 | All H-atom parameters refined |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0653P)2 + 0.7423P] where P = (Fo2 + 2Fc2)/3 |
2955 reflections | (Δ/σ)max < 0.001 |
184 parameters | Δρmax = 0.33 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
2C5H8N3+·C8H4O4−·2H2O | V = 2059.2 (11) Å3 |
Mr = 420.43 | Z = 4 |
Monoclinic, C2/c | Mo Kα radiation |
a = 15.795 (5) Å | µ = 0.10 mm−1 |
b = 13.083 (4) Å | T = 100 K |
c = 11.012 (4) Å | 0.42 × 0.36 × 0.03 mm |
β = 115.194 (5)° |
Bruker APEXII DUO CCD diffractometer | 2955 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 2148 reflections with I > 2σ(I) |
Tmin = 0.958, Tmax = 0.997 | Rint = 0.042 |
10343 measured reflections |
R[F2 > 2σ(F2)] = 0.043 | 0 restraints |
wR(F2) = 0.125 | All H-atom parameters refined |
S = 1.04 | Δρmax = 0.33 e Å−3 |
2955 reflections | Δρmin = −0.26 e Å−3 |
184 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.23077 (8) | 0.94380 (9) | 1.03746 (11) | 0.0227 (3) | |
N2 | 0.30262 (8) | 0.94315 (10) | 0.89459 (13) | 0.0256 (3) | |
N3 | 0.17815 (10) | 0.78666 (11) | 0.74285 (14) | 0.0330 (3) | |
C1 | 0.23819 (9) | 0.90400 (10) | 0.93023 (13) | 0.0192 (3) | |
C2 | 0.17516 (9) | 0.82430 (9) | 0.85688 (13) | 0.0210 (3) | |
C3 | 0.11106 (9) | 0.79131 (11) | 0.90331 (14) | 0.0249 (3) | |
C4 | 0.10585 (11) | 0.83570 (13) | 1.01540 (15) | 0.0313 (3) | |
C5 | 0.16621 (11) | 0.91224 (13) | 1.08149 (15) | 0.0310 (3) | |
O1 | 0.43751 (6) | 0.07071 (7) | 0.10193 (9) | 0.0225 (2) | |
O2 | 0.32273 (6) | 0.12167 (7) | 0.15491 (9) | 0.0225 (2) | |
C6 | 0.45346 (10) | 0.41720 (10) | 0.20469 (14) | 0.0242 (3) | |
C7 | 0.40590 (9) | 0.32537 (10) | 0.16012 (13) | 0.0201 (3) | |
C8 | 0.45249 (8) | 0.23274 (9) | 0.20552 (12) | 0.0160 (2) | |
C9 | 0.40094 (8) | 0.13405 (9) | 0.15149 (12) | 0.0168 (2) | |
O1W | 0.45043 (8) | 0.10881 (8) | 0.86130 (12) | 0.0315 (3) | |
H1 | 0.3388 (12) | 0.3242 (12) | 0.0959 (17) | 0.028 (4)* | |
H2 | 0.0692 (11) | 0.7346 (13) | 0.8557 (17) | 0.026 (4)* | |
H3 | 0.4209 (12) | 0.4807 (14) | 0.1749 (17) | 0.032 (4)* | |
H4 | 0.1689 (13) | 0.9496 (15) | 1.160 (2) | 0.043 (5)* | |
H5 | 0.3138 (13) | 0.9165 (14) | 0.8275 (19) | 0.033 (5)* | |
H6 | 0.2697 (12) | 1.0029 (15) | 1.0806 (18) | 0.036 (5)* | |
H7 | 0.3468 (13) | 0.9879 (15) | 0.9506 (19) | 0.039 (5)* | |
H8 | 0.0557 (13) | 0.8149 (14) | 1.044 (2) | 0.042 (5)* | |
H9 | 0.1404 (14) | 0.7328 (17) | 0.712 (2) | 0.046 (5)* | |
H10 | 0.2265 (14) | 0.7967 (14) | 0.723 (2) | 0.040 (5)* | |
H11 | 0.4555 (16) | 0.1035 (17) | 0.950 (3) | 0.064 (7)* | |
H12 | 0.4828 (16) | 0.0542 (18) | 0.850 (2) | 0.062 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0235 (6) | 0.0244 (6) | 0.0181 (5) | −0.0068 (5) | 0.0070 (4) | −0.0020 (4) |
N2 | 0.0237 (6) | 0.0281 (6) | 0.0260 (6) | −0.0104 (5) | 0.0116 (5) | −0.0096 (5) |
N3 | 0.0323 (7) | 0.0332 (7) | 0.0364 (7) | −0.0153 (6) | 0.0174 (6) | −0.0188 (6) |
C1 | 0.0186 (6) | 0.0182 (6) | 0.0175 (6) | −0.0001 (4) | 0.0043 (5) | 0.0016 (4) |
C2 | 0.0195 (6) | 0.0181 (6) | 0.0197 (6) | −0.0001 (5) | 0.0028 (5) | 0.0004 (5) |
C3 | 0.0232 (6) | 0.0223 (6) | 0.0224 (6) | −0.0060 (5) | 0.0033 (5) | 0.0024 (5) |
C4 | 0.0312 (7) | 0.0392 (8) | 0.0237 (7) | −0.0138 (6) | 0.0119 (6) | 0.0001 (6) |
C5 | 0.0348 (8) | 0.0393 (8) | 0.0223 (7) | −0.0128 (6) | 0.0153 (6) | −0.0043 (6) |
O1 | 0.0229 (5) | 0.0220 (5) | 0.0222 (5) | −0.0006 (4) | 0.0093 (4) | −0.0059 (4) |
O2 | 0.0205 (4) | 0.0227 (5) | 0.0253 (5) | −0.0041 (4) | 0.0106 (4) | −0.0029 (4) |
C6 | 0.0252 (7) | 0.0173 (6) | 0.0297 (7) | 0.0038 (5) | 0.0113 (6) | 0.0033 (5) |
C7 | 0.0191 (6) | 0.0200 (6) | 0.0196 (6) | 0.0017 (5) | 0.0068 (5) | 0.0022 (4) |
C8 | 0.0180 (6) | 0.0171 (6) | 0.0140 (5) | −0.0005 (4) | 0.0078 (4) | −0.0002 (4) |
C9 | 0.0178 (5) | 0.0173 (6) | 0.0124 (5) | 0.0007 (4) | 0.0036 (4) | 0.0006 (4) |
O1W | 0.0361 (6) | 0.0276 (6) | 0.0363 (6) | 0.0102 (4) | 0.0208 (5) | 0.0120 (4) |
N1—C1 | 1.3404 (17) | C4—H8 | 1.01 (2) |
N1—C5 | 1.3663 (18) | C5—H4 | 0.98 (2) |
N1—H6 | 0.98 (2) | O1—C9 | 1.2596 (15) |
N2—C1 | 1.3388 (17) | O2—C9 | 1.2623 (15) |
N2—H5 | 0.899 (19) | C6—C6i | 1.382 (3) |
N2—H7 | 0.92 (2) | C6—C7 | 1.3910 (19) |
N3—C2 | 1.3683 (19) | C6—H3 | 0.959 (18) |
N3—H9 | 0.89 (2) | C7—C8 | 1.3954 (17) |
N3—H10 | 0.89 (2) | C7—H1 | 0.993 (17) |
C1—C2 | 1.4304 (18) | C8—C8i | 1.400 (2) |
C2—C3 | 1.383 (2) | C8—C9 | 1.5072 (17) |
C3—C4 | 1.398 (2) | O1W—H11 | 0.95 (3) |
C3—H2 | 0.983 (17) | O1W—H12 | 0.91 (2) |
C4—C5 | 1.360 (2) | ||
C1—N1—C5 | 123.61 (12) | C5—C4—H8 | 119.7 (11) |
C1—N1—H6 | 117.6 (11) | C3—C4—H8 | 121.0 (11) |
C5—N1—H6 | 118.5 (10) | C4—C5—N1 | 119.44 (14) |
C1—N2—H5 | 122.2 (12) | C4—C5—H4 | 126.7 (11) |
C1—N2—H7 | 120.2 (11) | N1—C5—H4 | 113.8 (11) |
H5—N2—H7 | 116.0 (16) | C6i—C6—C7 | 120.25 (8) |
C2—N3—H9 | 111.0 (13) | C6i—C6—H3 | 119.9 (10) |
C2—N3—H10 | 122.9 (13) | C7—C6—H3 | 119.8 (10) |
H9—N3—H10 | 121.6 (18) | C6—C7—C8 | 120.03 (12) |
N2—C1—N1 | 118.16 (12) | C6—C7—H1 | 121.1 (10) |
N2—C1—C2 | 123.13 (12) | C8—C7—H1 | 118.9 (10) |
N1—C1—C2 | 118.67 (12) | C7—C8—C8i | 119.70 (7) |
N3—C2—C3 | 122.93 (12) | C7—C8—C9 | 119.26 (11) |
N3—C2—C1 | 119.54 (12) | C8i—C8—C9 | 120.95 (6) |
C3—C2—C1 | 117.49 (12) | O1—C9—O2 | 124.30 (11) |
C2—C3—C4 | 121.61 (13) | O1—C9—C8 | 117.67 (11) |
C2—C3—H2 | 118.0 (10) | O2—C9—C8 | 117.99 (11) |
C4—C3—H2 | 120.4 (10) | H11—O1W—H12 | 105.6 (19) |
C5—C4—C3 | 119.14 (13) | ||
C5—N1—C1—N2 | 178.22 (13) | C3—C4—C5—N1 | −0.3 (2) |
C5—N1—C1—C2 | 0.2 (2) | C1—N1—C5—C4 | 0.6 (2) |
N2—C1—C2—N3 | −1.5 (2) | C6i—C6—C7—C8 | −0.9 (2) |
N1—C1—C2—N3 | 176.36 (12) | C6—C7—C8—C8i | −0.9 (2) |
N2—C1—C2—C3 | −179.27 (13) | C6—C7—C8—C9 | −177.35 (12) |
N1—C1—C2—C3 | −1.39 (18) | C7—C8—C9—O1 | 126.40 (13) |
N3—C2—C3—C4 | −175.91 (14) | C8i—C8—C9—O1 | −50.01 (19) |
C1—C2—C3—C4 | 1.8 (2) | C7—C8—C9—O2 | −51.38 (16) |
C2—C3—C4—C5 | −0.9 (2) | C8i—C8—C9—O2 | 132.22 (15) |
Symmetry code: (i) −x+1, y, −z+1/2. |
Cg1 and Cg2 are the centroids of the C6–C8/C6A–C8A and N1/C1–C5 rings, respectively. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H5···O2ii | 0.90 (2) | 2.03 (2) | 2.9155 (19) | 169.0 (18) |
N1—H6···O2iii | 0.98 (2) | 1.790 (19) | 2.7565 (18) | 170.3 (19) |
N2—H7···O1iii | 0.92 (2) | 1.99 (2) | 2.8976 (19) | 168.1 (19) |
N3—H9···O1Wiv | 0.89 (2) | 2.09 (2) | 2.978 (2) | 179 (3) |
N3—H10···O2ii | 0.89 (2) | 2.23 (2) | 3.078 (2) | 158.8 (17) |
O1W—H11···O1v | 0.95 (3) | 1.86 (3) | 2.7878 (18) | 165 (3) |
O1W—H12···O1vi | 0.92 (2) | 1.99 (2) | 2.8641 (18) | 158.2 (19) |
C3—H2···O1Wvii | 0.984 (17) | 2.516 (18) | 3.369 (2) | 145.0 (14) |
C4—H8···Cg1iv | 1.01 (2) | 2.76 (2) | 3.629 (2) | 144.3 (15) |
C6—H3···Cg2viii | 0.959 (18) | 2.568 (18) | 3.497 (2) | 163.4 (14) |
Symmetry codes: (ii) x, −y+1, z+1/2; (iii) x, y+1, z+1; (iv) −x+1/2, y+1/2, −z+3/2; (v) x, y, z+1; (vi) −x+1, −y, −z+1; (vii) x−1/2, y+1/2, z; (viii) −x+1/2, −y+3/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | 2C5H8N3+·C8H4O4−·2H2O |
Mr | 420.43 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 100 |
a, b, c (Å) | 15.795 (5), 13.083 (4), 11.012 (4) |
β (°) | 115.194 (5) |
V (Å3) | 2059.2 (11) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.42 × 0.36 × 0.03 |
Data collection | |
Diffractometer | Bruker APEXII DUO CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.958, 0.997 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10343, 2955, 2148 |
Rint | 0.042 |
(sin θ/λ)max (Å−1) | 0.702 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.043, 0.125, 1.04 |
No. of reflections | 2955 |
No. of parameters | 184 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.33, −0.26 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
Cg1 and Cg2 are the centroids of the C6–C8/C6A–C8A and N1/C1–C5 rings, respectively. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H5···O2i | 0.90 (2) | 2.03 (2) | 2.9155 (19) | 169.0 (18) |
N1—H6···O2ii | 0.98 (2) | 1.790 (19) | 2.7565 (18) | 170.3 (19) |
N2—H7···O1ii | 0.92 (2) | 1.99 (2) | 2.8976 (19) | 168.1 (19) |
N3—H9···O1Wiii | 0.89 (2) | 2.09 (2) | 2.978 (2) | 179 (3) |
N3—H10···O2i | 0.89 (2) | 2.23 (2) | 3.078 (2) | 158.8 (17) |
O1W—H11···O1iv | 0.95 (3) | 1.86 (3) | 2.7878 (18) | 165 (3) |
O1W—H12···O1v | 0.92 (2) | 1.99 (2) | 2.8641 (18) | 158.2 (19) |
C3—H2···O1Wvi | 0.984 (17) | 2.516 (18) | 3.369 (2) | 145.0 (14) |
C4—H8···Cg1iii | 1.01 (2) | 2.76 (2) | 3.629 (2) | 144.3 (15) |
C6—H3···Cg2vii | 0.959 (18) | 2.568 (18) | 3.497 (2) | 163.4 (14) |
Symmetry codes: (i) x, −y+1, z+1/2; (ii) x, y+1, z+1; (iii) −x+1/2, y+1/2, −z+3/2; (iv) x, y, z+1; (v) −x+1, −y, −z+1; (vi) x−1/2, y+1/2, z; (vii) −x+1/2, −y+3/2, −z+1. |
Acknowledgements
MH, JHG and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University grant No. 1001/PFIZIK/811160. MH also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.
References
Banerjee, S. & Murugavel, R. (2004). Cryst. Growth Des. 4, 545–552. Web of Science CSD CrossRef CAS Google Scholar
Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107. CrossRef CAS Web of Science IUCr Journals Google Scholar
Gellert, R. W. & Hsu, I.-N. (1988). Acta Cryst. C44, 311–313. CSD CrossRef CAS Web of Science IUCr Journals Google Scholar
Hemamalini, M. & Fun, H.-K. (2010a). Acta Cryst. E66, o1418–o1419. Web of Science CSD CrossRef IUCr Journals Google Scholar
Hemamalini, M. & Fun, H.-K. (2010b). Acta Cryst. E66, o1480–o1481. Web of Science CSD CrossRef IUCr Journals Google Scholar
Hemamalini, M. & Fun, H.-K. (2010c). Acta Cryst. E66, o1496–o1497. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
2-Aminopyridine and its derivatives are amomg the most frequently used synthons in supramolecular chemistry based on hydrogen bonds (Gellert & Hsu, 1988; Banerjee & Murugavel, 2004). A series of similar complexes formed from 2-aminopyridine and carboxylates has been reported previously (Hemamalini & Fun, 2010a,b,c). The present work, 2,3-diaminopyridinium phthalate dihydrate, (2/1/1) (I), is a continuation of our structural study of complexes of the 2,3-diaminopyridinium system.
The asymmetric unit of the title compound, (I), contains one 2,3-diamino- pyridinium cation, a half of phthalate anion (which lies on a twofold axis; -x+1, y, -z+1/2) and a water molecule as shown in Fig. 1. The dihedral angle between the pyridine (N1/C1–C5) and benzene (C6–C8/ C6A–C8A) ring is 80.61 (7)°.
In the crystal structure (Fig. 2), the ion pairs and water molecules are connected via N—H···O, O—H···O and C—H···O (Table 1) hydrogen bonds forming a three-dimensional network. The crystal structure is further stabilized by C—H···π interactions involving the centroids of the C6–C8/C6A–C8A (Cg1) and N1/C1–C5 (Cg2) rings.