Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807021368/hk2241sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807021368/hk2241Isup2.hkl |
CCDC reference: 647023
Key indicators
- Single-crystal X-ray study
- T = 100 K
- Mean (C-C) = 0.002 Å
- R factor = 0.036
- wR factor = 0.097
- Data-to-parameter ratio = 17.6
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT154_ALERT_1_C The su's on the Cell Angles are Equal (x 10000) 100 Deg. PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 = 3 PLAT369_ALERT_2_C Long C(sp2)-C(sp2) Bond C5 - C7 ... 1.53 Ang. PLAT417_ALERT_2_C Short Inter D-H..H-D H3C .. H5A .. 2.11 Ang. PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd. # 2 C7 H3 N O4
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 1 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For general backgroud, see: Allen et al. (1987); Mendoza-Diaz et al. (2005); Chandrasekhar et al. (2001).
The title compound was synthesized by adding pyridine-2,3-dicarboxylic acid (10 mmol) to propane-1,3-diamine (10 mmol) in tetrahydrofuran (40 ml), and refluxing it. After a while, a white precipitate was obtained which was recrystallized to colorless crystals suitable for X-ray analysis.
H atoms were positioned geometrically, with O—H = 0.82 Å (for OH2), N—H = 0.91 Å (for NH3) and C—H = 0.95 and 0.99 Å for aromatic and methylene H, respectively, and constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C,O,N).
Pyridinedicarboxylic acids are applied as proton donors in ion pairs, as ligands in coordination compounds, and as hydrogen donor or acceptor in hydrogen bondings. However, their metal complexes have interesting properties in biological systems (Mendoza-Diaz et al., 2005).
The molecule of the title compound, (I), contains one dicationic and one dianionic fragments and also one water molecule (Fig. 1). The bond lengths and angles are within normal ranges (Allen et al., 1987). The two carboxylate groups of (pydc)2– fragment are perpendicular to each other.
As can be seen from the packing diagram (Fig. 2), the intramolecular N—H···O and intermolecular N—H···O, N—H···N, O—H···O and C—H···O hydrogen bonds (Table 1) and edge to face π-π stacking together with ion pairing are responsible for expanding the structure in three dimension resulting in a supramolecular network.
The bond distances and angles of C–H···π stacking are 2.81 Å (H···π) and 136° (C–H···π), which are within normal range (Chandrasekhar et al., 2001). Another notable feature of the structure as shown in Fig. 2, is that the hydrogen bonds between water molecules, NH3+ tail of diamine and O atom of carboxylate group (i.e. two O5, two N3 and two O3 atoms and the related H atoms) form a 12-membered cyclic arrangement with a centre of symmetry in the middle of the ring.
For general backgroud, see: Allen et al. (1987); Mendoza-Diaz et al. (2005); Chandrasekhar et al. (2001).
Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2005); software used to prepare material for publication: SHELXTL.
C3H12N22+·C7H3NO42−·H2O | Z = 2 |
Mr = 259.27 | F(000) = 276 |
Triclinic, P1 | Dx = 1.424 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.4274 (5) Å | Cell parameters from 265 reflections |
b = 8.6176 (5) Å | θ = 3–28° |
c = 10.7314 (7) Å | µ = 0.12 mm−1 |
α = 109.989 (1)° | T = 100 K |
β = 102.225 (1)° | Prism, colourless |
γ = 100.883 (1)° | 0.24 × 0.22 × 0.18 mm |
V = 604.81 (7) Å3 |
Bruker APEXII CCD area-detector diffractometer | 2897 independent reflections |
Radiation source: fine-focus sealed tube | 2467 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
ω scans | θmax = 28.0°, θmin = 2.1° |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | h = −9→9 |
Tmin = 0.970, Tmax = 0.978 | k = −11→11 |
6110 measured reflections | l = −13→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)] = 0.036 | Hydrogen site location: constr |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0478P)2 + 0.1817P] where P = (Fo2 + 2Fc2)/3 |
2897 reflections | (Δ/σ)max < 0.001 |
165 parameters | Δρmax = 0.38 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
C3H12N22+·C7H3NO42−·H2O | γ = 100.883 (1)° |
Mr = 259.27 | V = 604.81 (7) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.4274 (5) Å | Mo Kα radiation |
b = 8.6176 (5) Å | µ = 0.12 mm−1 |
c = 10.7314 (7) Å | T = 100 K |
α = 109.989 (1)° | 0.24 × 0.22 × 0.18 mm |
β = 102.225 (1)° |
Bruker APEXII CCD area-detector diffractometer | 2897 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2005) | 2467 reflections with I > 2σ(I) |
Tmin = 0.970, Tmax = 0.978 | Rint = 0.022 |
6110 measured reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.38 e Å−3 |
2897 reflections | Δρmin = −0.24 e Å−3 |
165 parameters |
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 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 > σ(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 | ||
O1 | 0.97996 (13) | 0.66664 (11) | 0.41529 (9) | 0.01712 (19) | |
O2 | 1.21462 (12) | 0.91436 (10) | 0.50032 (8) | 0.01534 (19) | |
O3 | 1.32210 (12) | 0.61030 (11) | 0.31424 (8) | 0.01571 (19) | |
O4 | 1.39865 (14) | 0.59160 (13) | 0.11966 (10) | 0.0227 (2) | |
N1 | 1.10608 (14) | 0.71092 (12) | 0.03480 (10) | 0.0140 (2) | |
C1 | 0.97376 (17) | 0.78571 (15) | −0.00249 (12) | 0.0153 (2) | |
H1A | 0.9425 | 0.7817 | −0.0943 | 0.018* | |
C2 | 0.88011 (17) | 0.86906 (15) | 0.08756 (12) | 0.0163 (2) | |
H2A | 0.7908 | 0.9249 | 0.0588 | 0.020* | |
C3 | 0.91878 (17) | 0.86966 (15) | 0.21982 (12) | 0.0150 (2) | |
H3A | 0.8557 | 0.9249 | 0.2829 | 0.018* | |
C4 | 1.05220 (16) | 0.78750 (14) | 0.25870 (11) | 0.0119 (2) | |
C5 | 1.14535 (16) | 0.71214 (14) | 0.16337 (11) | 0.0116 (2) | |
C6 | 1.08930 (16) | 0.78848 (14) | 0.40348 (12) | 0.0125 (2) | |
C7 | 1.30215 (17) | 0.63029 (14) | 0.20165 (12) | 0.0135 (2) | |
N2 | 0.69146 (14) | 0.43762 (12) | 0.16715 (10) | 0.0141 (2) | |
H2B | 0.7342 | 0.4160 | 0.0912 | 0.017* | |
H2C | 0.7898 | 0.5099 | 0.2445 | 0.017* | |
H2D | 0.5948 | 0.4876 | 0.1572 | 0.017* | |
N3 | 0.37974 (15) | 0.18365 (13) | 0.44053 (10) | 0.0153 (2) | |
H3B | 0.3267 | 0.0846 | 0.4484 | 0.018* | |
H3C | 0.2909 | 0.2425 | 0.4341 | 0.018* | |
H3D | 0.4825 | 0.2498 | 0.5167 | 0.018* | |
C8 | 0.61920 (17) | 0.27374 (15) | 0.18108 (12) | 0.0151 (2) | |
H8A | 0.7223 | 0.2162 | 0.1869 | 0.018* | |
H8B | 0.5102 | 0.1961 | 0.0980 | 0.018* | |
C9 | 0.55396 (17) | 0.30690 (15) | 0.31028 (12) | 0.0152 (2) | |
H9A | 0.4709 | 0.3846 | 0.3133 | 0.018* | |
H9B | 0.6677 | 0.3655 | 0.3937 | 0.018* | |
C10 | 0.44394 (17) | 0.14129 (15) | 0.31345 (12) | 0.0151 (2) | |
H10A | 0.3310 | 0.0806 | 0.2295 | 0.018* | |
H10B | 0.5275 | 0.0645 | 0.3141 | 0.018* | |
O5 | 0.09016 (13) | 0.32465 (11) | 0.34573 (9) | 0.0181 (2) | |
H5A | 0.0514 | 0.3400 | 0.4139 | 0.022* | |
H5B | 0.1245 | 0.4204 | 0.3448 | 0.022* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0195 (4) | 0.0172 (4) | 0.0141 (4) | 0.0004 (3) | 0.0058 (3) | 0.0077 (3) |
O2 | 0.0180 (4) | 0.0143 (4) | 0.0116 (4) | 0.0020 (3) | 0.0033 (3) | 0.0045 (3) |
O3 | 0.0190 (4) | 0.0167 (4) | 0.0132 (4) | 0.0066 (3) | 0.0045 (3) | 0.0074 (3) |
O4 | 0.0254 (5) | 0.0335 (5) | 0.0210 (5) | 0.0182 (4) | 0.0135 (4) | 0.0155 (4) |
N1 | 0.0170 (5) | 0.0128 (5) | 0.0113 (5) | 0.0027 (4) | 0.0043 (4) | 0.0047 (4) |
C1 | 0.0183 (6) | 0.0151 (5) | 0.0113 (5) | 0.0031 (4) | 0.0019 (4) | 0.0060 (4) |
C2 | 0.0152 (6) | 0.0165 (6) | 0.0174 (6) | 0.0054 (5) | 0.0027 (5) | 0.0079 (5) |
C3 | 0.0159 (6) | 0.0146 (5) | 0.0146 (5) | 0.0044 (4) | 0.0059 (4) | 0.0052 (4) |
C4 | 0.0128 (5) | 0.0100 (5) | 0.0112 (5) | 0.0003 (4) | 0.0033 (4) | 0.0040 (4) |
C5 | 0.0129 (5) | 0.0100 (5) | 0.0107 (5) | 0.0007 (4) | 0.0033 (4) | 0.0043 (4) |
C6 | 0.0145 (5) | 0.0136 (5) | 0.0121 (5) | 0.0066 (4) | 0.0059 (4) | 0.0056 (4) |
C7 | 0.0144 (5) | 0.0106 (5) | 0.0136 (5) | 0.0023 (4) | 0.0035 (4) | 0.0038 (4) |
N2 | 0.0152 (5) | 0.0150 (5) | 0.0123 (5) | 0.0031 (4) | 0.0053 (4) | 0.0056 (4) |
N3 | 0.0165 (5) | 0.0147 (5) | 0.0150 (5) | 0.0024 (4) | 0.0038 (4) | 0.0079 (4) |
C8 | 0.0165 (6) | 0.0131 (5) | 0.0143 (5) | 0.0027 (4) | 0.0044 (4) | 0.0048 (4) |
C9 | 0.0170 (6) | 0.0133 (5) | 0.0148 (5) | 0.0025 (4) | 0.0053 (4) | 0.0057 (4) |
C10 | 0.0155 (5) | 0.0149 (5) | 0.0142 (5) | 0.0033 (4) | 0.0033 (4) | 0.0062 (4) |
O5 | 0.0245 (5) | 0.0168 (4) | 0.0158 (4) | 0.0061 (4) | 0.0098 (4) | 0.0077 (3) |
O1—C6 | 1.2612 (14) | N2—H2C | 0.9100 |
O2—C6 | 1.2495 (14) | N2—H2D | 0.9100 |
O3—C7 | 1.2601 (14) | N3—C10 | 1.4905 (15) |
O4—C7 | 1.2473 (15) | N3—H3B | 0.9100 |
N1—C1 | 1.3380 (15) | N3—H3C | 0.9100 |
N1—C5 | 1.3444 (14) | N3—H3D | 0.9100 |
C1—C2 | 1.3902 (17) | C8—C9 | 1.5181 (16) |
C1—H1A | 0.9500 | C8—H8A | 0.9900 |
C2—C3 | 1.3853 (16) | C8—H8B | 0.9900 |
C2—H2A | 0.9500 | C9—C10 | 1.5199 (16) |
C3—C4 | 1.3961 (16) | C9—H9A | 0.9900 |
C3—H3A | 0.9500 | C9—H9B | 0.9900 |
C4—C5 | 1.4008 (15) | C10—H10A | 0.9900 |
C4—C6 | 1.5162 (15) | C10—H10B | 0.9900 |
C5—C7 | 1.5258 (15) | O5—H5A | 0.8200 |
N2—C8 | 1.4822 (15) | O5—H5B | 0.8200 |
N2—H2B | 0.9100 | ||
C1—N1—C5 | 118.43 (10) | H2C—N2—H2D | 109.5 |
N1—C1—C2 | 122.72 (11) | C10—N3—H3B | 109.5 |
N1—C1—H1A | 118.6 | C10—N3—H3C | 109.5 |
C2—C1—H1A | 118.6 | H3B—N3—H3C | 109.5 |
C3—C2—C1 | 119.13 (11) | C10—N3—H3D | 109.5 |
C3—C2—H2A | 120.4 | H3B—N3—H3D | 109.5 |
C1—C2—H2A | 120.4 | H3C—N3—H3D | 109.5 |
C2—C3—C4 | 118.75 (11) | N2—C8—C9 | 110.58 (9) |
C2—C3—H3A | 120.6 | N2—C8—H8A | 109.5 |
C4—C3—H3A | 120.6 | C9—C8—H8A | 109.5 |
C3—C4—C5 | 118.43 (10) | N2—C8—H8B | 109.5 |
C3—C4—C6 | 117.43 (10) | C9—C8—H8B | 109.5 |
C5—C4—C6 | 124.13 (10) | H8A—C8—H8B | 108.1 |
N1—C5—C4 | 122.47 (10) | C8—C9—C10 | 112.02 (9) |
N1—C5—C7 | 116.06 (10) | C8—C9—H9A | 109.2 |
C4—C5—C7 | 121.45 (10) | C10—C9—H9A | 109.2 |
O2—C6—O1 | 126.29 (11) | C8—C9—H9B | 109.2 |
O2—C6—C4 | 117.55 (10) | C10—C9—H9B | 109.2 |
O1—C6—C4 | 115.97 (10) | H9A—C9—H9B | 107.9 |
O4—C7—O3 | 126.58 (11) | N3—C10—C9 | 109.16 (9) |
O4—C7—C5 | 117.09 (10) | N3—C10—H10A | 109.8 |
O3—C7—C5 | 116.33 (10) | C9—C10—H10A | 109.8 |
C8—N2—H2B | 109.5 | N3—C10—H10B | 109.8 |
C8—N2—H2C | 109.5 | C9—C10—H10B | 109.8 |
H2B—N2—H2C | 109.5 | H10A—C10—H10B | 108.3 |
C8—N2—H2D | 109.5 | H5A—O5—H5B | 105.4 |
H2B—N2—H2D | 109.5 | ||
C5—N1—C1—C2 | 2.11 (17) | C3—C4—C6—O2 | −87.25 (13) |
N1—C1—C2—C3 | −2.61 (18) | C5—C4—C6—O2 | 91.67 (14) |
C1—C2—C3—C4 | 0.55 (17) | C3—C4—C6—O1 | 87.95 (13) |
C2—C3—C4—C5 | 1.79 (17) | C5—C4—C6—O1 | −93.12 (13) |
C2—C3—C4—C6 | −179.22 (10) | N1—C5—C7—O4 | 9.82 (15) |
C1—N1—C5—C4 | 0.43 (17) | C4—C5—C7—O4 | −168.65 (11) |
C1—N1—C5—C7 | −178.02 (10) | N1—C5—C7—O3 | −170.88 (10) |
C3—C4—C5—N1 | −2.37 (17) | C4—C5—C7—O3 | 10.65 (16) |
C6—C4—C5—N1 | 178.71 (10) | N2—C8—C9—C10 | 168.92 (9) |
C3—C4—C5—C7 | 176.00 (10) | C8—C9—C10—N3 | −178.42 (9) |
C6—C4—C5—C7 | −2.92 (17) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2B···O4i | 0.91 | 2.24 | 2.918 (1) | 131 |
N2—H2B···N1i | 0.91 | 2.14 | 2.967 (2) | 150 |
N2—H2C···O1 | 0.91 | 1.92 | 2.823 (1) | 175 |
N2—H2D···O4ii | 0.91 | 1.89 | 2.798 (2) | 174 |
N3—H3B···O2iii | 0.91 | 1.86 | 2.752 (2) | 168 |
N3—H3C···O5 | 0.91 | 1.97 | 2.836 (2) | 158 |
N3—H3D···O3iv | 0.91 | 1.89 | 2.799 (1) | 174 |
O5—H5A···O1v | 0.82 | 1.91 | 2.702 (1) | 161 |
O5—H5B···O1ii | 0.82 | 2.52 | 3.094 (1) | 128 |
O5—H5B···O3ii | 0.82 | 2.15 | 2.890 (1) | 151 |
C10—H10B···O2iv | 0.99 | 2.38 | 3.102 (2) | 129 |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z; (iii) x−1, y−1, z; (iv) −x+2, −y+1, −z+1; (v) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C3H12N22+·C7H3NO42−·H2O |
Mr | 259.27 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 100 |
a, b, c (Å) | 7.4274 (5), 8.6176 (5), 10.7314 (7) |
α, β, γ (°) | 109.989 (1), 102.225 (1), 100.883 (1) |
V (Å3) | 604.81 (7) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.24 × 0.22 × 0.18 |
Data collection | |
Diffractometer | Bruker APEXII CCD area-detector |
Absorption correction | Multi-scan (SADABS; Bruker, 2005) |
Tmin, Tmax | 0.970, 0.978 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6110, 2897, 2467 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.661 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.097, 1.04 |
No. of reflections | 2897 |
No. of parameters | 165 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.38, −0.24 |
Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2005), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 2005), SHELXTL.
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2B···O4i | 0.91 | 2.24 | 2.918 (1) | 131 |
N2—H2B···N1i | 0.91 | 2.14 | 2.967 (2) | 150 |
N2—H2C···O1 | 0.91 | 1.92 | 2.823 (1) | 175 |
N2—H2D···O4ii | 0.91 | 1.89 | 2.798 (2) | 174 |
N3—H3B···O2iii | 0.91 | 1.86 | 2.752 (2) | 168 |
N3—H3C···O5 | 0.91 | 1.97 | 2.836 (2) | 158 |
N3—H3D···O3iv | 0.91 | 1.89 | 2.799 (1) | 174 |
O5—H5A···O1v | 0.82 | 1.91 | 2.702 (1) | 161 |
O5—H5B···O1ii | 0.82 | 2.52 | 3.094 (1) | 128 |
O5—H5B···O3ii | 0.82 | 2.15 | 2.890 (1) | 151 |
C10—H10B···O2iv | 0.99 | 2.38 | 3.102 (2) | 129 |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x−1, y, z; (iii) x−1, y−1, z; (iv) −x+2, −y+1, −z+1; (v) −x+1, −y+1, −z+1. |
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Pyridinedicarboxylic acids are applied as proton donors in ion pairs, as ligands in coordination compounds, and as hydrogen donor or acceptor in hydrogen bondings. However, their metal complexes have interesting properties in biological systems (Mendoza-Diaz et al., 2005).
The molecule of the title compound, (I), contains one dicationic and one dianionic fragments and also one water molecule (Fig. 1). The bond lengths and angles are within normal ranges (Allen et al., 1987). The two carboxylate groups of (pydc)2– fragment are perpendicular to each other.
As can be seen from the packing diagram (Fig. 2), the intramolecular N—H···O and intermolecular N—H···O, N—H···N, O—H···O and C—H···O hydrogen bonds (Table 1) and edge to face π-π stacking together with ion pairing are responsible for expanding the structure in three dimension resulting in a supramolecular network.
The bond distances and angles of C–H···π stacking are 2.81 Å (H···π) and 136° (C–H···π), which are within normal range (Chandrasekhar et al., 2001). Another notable feature of the structure as shown in Fig. 2, is that the hydrogen bonds between water molecules, NH3+ tail of diamine and O atom of carboxylate group (i.e. two O5, two N3 and two O3 atoms and the related H atoms) form a 12-membered cyclic arrangement with a centre of symmetry in the middle of the ring.