Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807045230/hk2325sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807045230/hk2325Isup2.hkl |
CCDC reference: 1233790
Key indicators
- Single-crystal X-ray study
- T = 273 K
- Mean (C-C) = 0.005 Å
- R factor = 0.056
- wR factor = 0.192
- Data-to-parameter ratio = 11.3
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT230_ALERT_2_B Hirshfeld Test Diff for O6 - N4 .. 13.50 su PLAT230_ALERT_2_B Hirshfeld Test Diff for O7 - N4 .. 9.69 su PLAT230_ALERT_2_B Hirshfeld Test Diff for N1 - C3 .. 8.19 su PLAT230_ALERT_2_B Hirshfeld Test Diff for N1 - C4 .. 8.56 su PLAT230_ALERT_2_B Hirshfeld Test Diff for N4 - C4 .. 8.29 su PLAT430_ALERT_2_B Short Inter D...A Contact O5 .. O7 .. 2.80 Ang. PLAT430_ALERT_2_B Short Inter D...A Contact O6 .. O6 .. 2.57 Ang.
Alert level C PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.97 PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for N1 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C4 PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.11 PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ... 5
Alert level G PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 3
0 ALERT level A = In general: serious problem 7 ALERT level B = Potentially serious problem 6 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 10 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For general background, see: Carter et al. (1998); Lowe et al. (1999); Pai et al. (2000); Swarnabala & Rajasekharan (1998); Zhao et al. (2005). For bond-length data, see: Allen et al. (1987).
Crystals of the title compound were synthesized using hydrothermal method in a 23 ml Teflon-lined Parr bomb. Neodymium(III) nitrate hexahydrate (219.1 mg, 0.5 mmol), 3-hydroxy-2,4,6-trinitropyridine (230.2 mg, 1 mmol) and distilled water (8 g) were placed into the bomb and sealed. The bomb was then heated under autogenous pressure up to 443 K over the course of 7 d and allowed to cool at room temperature for 24 h. Upon opening the bomb, a clear colorless solution was decanted from small colorless crystals. These crystals were washed with distilled water followed by ethanol, and allowed to air-dry at room temperature.
H8A and H8B (for OH2) were located were located in difference syntheses and refined isotropically [O—H = 0.85 (3) and 0.85 (3) Å, Uiso(H) = 0.092 (16) and 0.15 (2) Å2]. The remaining H atoms were positioned geometrically, with O—H = 0.82 Å (for OH) and C—H = 0.93 Å for aromatic H, and constrained to ride on their parent atoms, with Uiso(H) = xUeq(C,O), where x = 1.2 for aromatic H, and x = 1.5 for OH H atoms.
Due to pyridyl groups are one of the most important classes of biological ligands, the coordination of metal–pyridyl groups complexes are of critical importance in biological systems, organic materials and coordination chemistry. Recently, pyridyl groups with variable coordination modes have been used to construct metal–organic supramolecular structures (Carter et al., 1998; Lowe et al., 1999; Pai et al., 2000; Swarnabala & Rajasekharan, 1998; Zhao et al., 2005). We originally attempted to synthesize complexes featuring Nd metal chains by reaction of the neodymium(III) ion with 3-hydroxy-2,4,6-trinitropyridine ligand. Unfortunately, we obtained only the title compound, (I), and we report herein its crystal structure.
In the molecule of (I) (Fig. 1), the ligand bond lengths and angles are within normal ranges (Allen et al., 1987). It contains one C5H2N4O7 molecule and one H2O molecule.
In the crystal structure, intermolecular O—H···O hydrogen bonds (Table 1, Fig. 2) result in the formation of a supramolecular network structure; intramolecular O—H···O and O—H···N hydrogen bonds (Table 1) are also present.
For general background, see: Carter et al. (1998); Lowe et al. (1999); Pai et al. (2000); Swarnabala & Rajasekharan (1998); Zhao et al. (2005). For bond-length data, see: Allen et al. (1987).
Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Siemens, 1996); software used to prepare material for publication: SHELXTL (Siemens, 1996).
C5H2N4O7·H2O | F(000) = 1008 |
Mr = 248.12 | Dx = 1.805 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 1493 reflections |
a = 25.103 (2) Å | θ = 2.8–26.8° |
b = 6.4103 (17) Å | µ = 0.18 mm−1 |
c = 12.2307 (11) Å | T = 273 K |
β = 111.897 (4)° | Prism, colourless |
V = 1826.1 (5) Å3 | 0.24 × 0.15 × 0.14 mm |
Z = 8 |
Bruker SMART CCD area-detector diffractometer | 1841 independent reflections |
Radiation source: fine-focus sealed tube | 955 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.031 |
φ and ω scans | θmax = 26.6°, θmin = 3.6° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −31→31 |
Tmin = 0.959, Tmax = 0.975 | k = −7→8 |
5964 measured reflections | l = −15→15 |
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)] = 0.056 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.192 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | w = 1/[σ2(Fo2) + (0.1224P)2 + 0.3617P] where P = (Fo2 + 2Fc2)/3 |
1841 reflections | (Δ/σ)max < 0.001 |
163 parameters | Δρmax = 0.56 e Å−3 |
3 restraints | Δρmin = −0.45 e Å−3 |
C5H2N4O7·H2O | V = 1826.1 (5) Å3 |
Mr = 248.12 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 25.103 (2) Å | µ = 0.18 mm−1 |
b = 6.4103 (17) Å | T = 273 K |
c = 12.2307 (11) Å | 0.24 × 0.15 × 0.14 mm |
β = 111.897 (4)° |
Bruker SMART CCD area-detector diffractometer | 1841 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 955 reflections with I > 2σ(I) |
Tmin = 0.959, Tmax = 0.975 | Rint = 0.031 |
5964 measured reflections |
R[F2 > 2σ(F2)] = 0.056 | 3 restraints |
wR(F2) = 0.192 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.56 e Å−3 |
1841 reflections | Δρmin = −0.45 e Å−3 |
163 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 | 0.40218 (10) | 0.2101 (5) | 0.7293 (2) | 0.0667 (8) | |
H1 | 0.4369 | 0.2174 | 0.7461 | 0.100* | |
O2 | 0.29261 (11) | 0.1309 (5) | 0.6307 (2) | 0.0726 (8) | |
O3 | 0.24198 (10) | 0.3054 (5) | 0.7038 (2) | 0.0707 (8) | |
O4 | 0.30592 (11) | 0.3719 (5) | 1.1123 (2) | 0.0767 (8) | |
O5 | 0.39222 (13) | 0.3006 (5) | 1.2180 (2) | 0.0890 (10) | |
O6 | 0.50769 (12) | 0.2168 (6) | 0.8601 (2) | 0.0954 (12) | |
O7 | 0.53307 (10) | 0.2528 (4) | 1.0474 (2) | 0.0630 (7) | |
O8 | 0.13152 (11) | 0.2710 (4) | 0.5274 (3) | 0.0665 (8) | |
H8A | 0.1318 (19) | 0.287 (7) | 0.4587 (15) | 0.092 (16)* | |
H8B | 0.1671 (6) | 0.297 (10) | 0.563 (3) | 0.15 (2)* | |
N1 | 0.42327 (15) | 0.2687 (5) | 1.0332 (3) | 0.0692 (9) | |
N2 | 0.28669 (12) | 0.2259 (5) | 0.7093 (2) | 0.0563 (8) | |
N3 | 0.35432 (14) | 0.3203 (5) | 1.1253 (3) | 0.0598 (8) | |
N4 | 0.49590 (14) | 0.2382 (6) | 0.9437 (3) | 0.0779 (10) | |
C1 | 0.33555 (14) | 0.2442 (5) | 0.8198 (3) | 0.0481 (8) | |
C2 | 0.32265 (14) | 0.2744 (5) | 0.9165 (3) | 0.0480 (8) | |
H2 | 0.2848 | 0.2878 | 0.9109 | 0.058* | |
C3 | 0.36664 (14) | 0.2841 (5) | 1.0210 (3) | 0.0492 (8) | |
C4 | 0.43536 (13) | 0.2449 (5) | 0.9352 (3) | 0.0489 (8) | |
C5 | 0.39105 (14) | 0.2309 (5) | 0.8244 (3) | 0.0480 (8) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0352 (13) | 0.113 (2) | 0.0514 (14) | −0.0003 (12) | 0.0153 (11) | −0.0023 (12) |
O2 | 0.0502 (15) | 0.109 (2) | 0.0540 (14) | −0.0057 (14) | 0.0138 (12) | −0.0143 (14) |
O3 | 0.0319 (13) | 0.110 (2) | 0.0648 (16) | 0.0097 (12) | 0.0122 (11) | 0.0058 (13) |
O4 | 0.0545 (17) | 0.112 (2) | 0.0726 (17) | 0.0047 (15) | 0.0344 (14) | −0.0079 (15) |
O5 | 0.072 (2) | 0.145 (3) | 0.0465 (16) | 0.0151 (17) | 0.0180 (15) | −0.0027 (15) |
O6 | 0.0408 (15) | 0.202 (4) | 0.0491 (16) | 0.0026 (16) | 0.0234 (13) | 0.0010 (16) |
O7 | 0.0355 (14) | 0.0908 (19) | 0.0513 (14) | −0.0015 (11) | 0.0030 (11) | −0.0005 (11) |
O8 | 0.0378 (14) | 0.0893 (19) | 0.0668 (18) | −0.0018 (12) | 0.0131 (12) | −0.0036 (14) |
N1 | 0.062 (2) | 0.076 (2) | 0.069 (2) | −0.0007 (15) | 0.0238 (17) | 0.0008 (15) |
N2 | 0.0366 (16) | 0.080 (2) | 0.0485 (17) | −0.0058 (13) | 0.0118 (13) | 0.0061 (14) |
N3 | 0.056 (2) | 0.073 (2) | 0.0537 (18) | −0.0009 (15) | 0.0242 (16) | −0.0046 (13) |
N4 | 0.052 (2) | 0.098 (3) | 0.077 (2) | −0.0010 (16) | 0.016 (2) | 0.0065 (17) |
C1 | 0.0391 (18) | 0.057 (2) | 0.0431 (17) | −0.0001 (13) | 0.0100 (14) | 0.0041 (13) |
C2 | 0.0362 (18) | 0.0538 (19) | 0.0544 (19) | 0.0019 (13) | 0.0173 (15) | 0.0044 (13) |
C3 | 0.0435 (19) | 0.0597 (19) | 0.0484 (18) | 0.0023 (14) | 0.0216 (15) | 0.0011 (14) |
C4 | 0.0344 (17) | 0.064 (2) | 0.0502 (19) | 0.0004 (14) | 0.0178 (15) | 0.0016 (14) |
C5 | 0.0371 (17) | 0.065 (2) | 0.0426 (17) | 0.0012 (14) | 0.0159 (14) | −0.0012 (13) |
O1—C5 | 1.300 (4) | N1—C4 | 1.350 (5) |
O1—H1 | 0.8200 | N1—C3 | 1.377 (5) |
O2—N2 | 1.193 (4) | N2—C1 | 1.453 (4) |
O3—N2 | 1.212 (4) | N3—C3 | 1.440 (4) |
O4—N3 | 1.211 (4) | N4—C4 | 1.485 (5) |
O5—N3 | 1.184 (4) | C1—C2 | 1.351 (5) |
O6—N4 | 1.174 (4) | C1—C5 | 1.376 (5) |
O7—N4 | 1.268 (4) | C2—C3 | 1.343 (5) |
O8—H8A | 0.85 (3) | C2—H2 | 0.9300 |
O8—H8B | 0.85 (3) | C4—C5 | 1.399 (5) |
C5—O1—H1 | 109.5 | C2—C1—N2 | 115.6 (3) |
H8A—O8—H8B | 95 (4) | C5—C1—N2 | 121.6 (3) |
H8B—O8—H8A | 95 (4) | C3—C2—C1 | 117.3 (3) |
C4—N1—C3 | 118.5 (3) | C3—C2—H2 | 121.3 |
O2—N2—O3 | 124.2 (3) | C1—C2—H2 | 121.3 |
O2—N2—C1 | 118.4 (3) | C2—C3—N1 | 123.3 (3) |
O3—N2—C1 | 117.4 (3) | C2—C3—N3 | 118.6 (3) |
O5—N3—O4 | 124.4 (3) | N1—C3—N3 | 118.1 (3) |
O5—N3—C3 | 118.0 (3) | N1—C4—C5 | 120.4 (3) |
O4—N3—C3 | 117.6 (3) | N1—C4—N4 | 120.3 (3) |
O6—N4—O7 | 123.4 (3) | C5—C4—N4 | 119.3 (3) |
O6—N4—C4 | 121.8 (3) | O1—C5—C1 | 121.5 (3) |
O7—N4—C4 | 114.8 (3) | O1—C5—C4 | 121.0 (3) |
C2—C1—C5 | 122.9 (3) | C1—C5—C4 | 117.6 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O6 | 0.82 | 1.80 | 2.533 (3) | 148 |
O1—H1···N4 | 0.82 | 2.32 | 2.800 (4) | 118 |
O8—H8B···O3 | 0.85 (3) | 2.02 (2) | 2.816 (4) | 155 (4) |
O1—H1···O6i | 0.82 | 2.23 | 2.857 (4) | 134 |
O8—H8A···O1ii | 0.85 (3) | 2.13 (2) | 2.934 (4) | 157 (4) |
O8—H8A···O2ii | 0.85 (3) | 2.57 (3) | 3.242 (4) | 137 (4) |
Symmetry codes: (i) −x+1, y, −z+3/2; (ii) −x+1/2, −y+1/2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C5H2N4O7·H2O |
Mr | 248.12 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 273 |
a, b, c (Å) | 25.103 (2), 6.4103 (17), 12.2307 (11) |
β (°) | 111.897 (4) |
V (Å3) | 1826.1 (5) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.18 |
Crystal size (mm) | 0.24 × 0.15 × 0.14 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.959, 0.975 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5964, 1841, 955 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.629 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.056, 0.192, 1.03 |
No. of reflections | 1841 |
No. of parameters | 163 |
No. of restraints | 3 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.56, −0.45 |
Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Siemens, 1996).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1···O6 | 0.82 | 1.80 | 2.533 (3) | 148 |
O1—H1···N4 | 0.82 | 2.32 | 2.800 (4) | 118 |
O8—H8B···O3 | 0.85 (3) | 2.024 (19) | 2.816 (4) | 155 (4) |
O1—H1···O6i | 0.82 | 2.23 | 2.857 (4) | 134 |
O8—H8A···O1ii | 0.85 (3) | 2.134 (17) | 2.934 (4) | 157 (4) |
O8—H8A···O2ii | 0.85 (3) | 2.57 (3) | 3.242 (4) | 137 (4) |
Symmetry codes: (i) −x+1, y, −z+3/2; (ii) −x+1/2, −y+1/2, −z+1. |
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Due to pyridyl groups are one of the most important classes of biological ligands, the coordination of metal–pyridyl groups complexes are of critical importance in biological systems, organic materials and coordination chemistry. Recently, pyridyl groups with variable coordination modes have been used to construct metal–organic supramolecular structures (Carter et al., 1998; Lowe et al., 1999; Pai et al., 2000; Swarnabala & Rajasekharan, 1998; Zhao et al., 2005). We originally attempted to synthesize complexes featuring Nd metal chains by reaction of the neodymium(III) ion with 3-hydroxy-2,4,6-trinitropyridine ligand. Unfortunately, we obtained only the title compound, (I), and we report herein its crystal structure.
In the molecule of (I) (Fig. 1), the ligand bond lengths and angles are within normal ranges (Allen et al., 1987). It contains one C5H2N4O7 molecule and one H2O molecule.
In the crystal structure, intermolecular O—H···O hydrogen bonds (Table 1, Fig. 2) result in the formation of a supramolecular network structure; intramolecular O—H···O and O—H···N hydrogen bonds (Table 1) are also present.