Literature DB >> 21588952

3,4-Diaminopyridinium 2-carboxy-4,6-dinitrophenolate.

Madhukar Hemamalini1, Hoong-Kun Fun.   

Abstract

In the title salt, C(5)H(8)N(3) (+)·C(7)H(3)N(2)O(7) (-), the pyridine N atom of the 3,4-diamino-pyridine mol-ecule is protonated. The 3,5-dinitro-salicylate anion shows whole-mol-ecule disorder over two orientations with a refined occupancy ratio of 0.875 (4): 0.125 (4). In the crystal, the cations and anions are connected by inter-molecular N-H⋯O and C-H⋯O hydrogen bonds, forming a three-dimensional network.

Entities:  

Year:  2010        PMID: 21588952      PMCID: PMC3009103          DOI: 10.1107/S1600536810038936

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For applications of diamino­pyridine, see: Abu Zuhri & Cox (1989 ▶); Inuzuka & Fujimoto (1990 ▶); El-Mossalamy (2001 ▶). For related structures, see: Rubin-Preminger & Englert (2007 ▶); Koleva et al. (2007 ▶); Koleva et al. (2008 ▶). For reference bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C5H8N3C7H3N2O7 − M = 337.26 Monoclinic, a = 9.1187 (4) Å b = 11.3569 (5) Å c = 13.1343 (6) Å β = 98.204 (4)° V = 1346.27 (10) Å3 Z = 4 Mo Kα radiation μ = 0.14 mm−1 T = 100 K 0.52 × 0.11 × 0.10 mm

Data collection

Bruker SMART APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.931, T max = 0.986 10195 measured reflections 2785 independent reflections 1979 reflections with I > 2σ(I) R int = 0.064

Refinement

R[F 2 > 2σ(F 2)] = 0.070 wR(F 2) = 0.162 S = 1.12 2785 reflections 287 parameters 526 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.46 e Å−3 Δρmin = −0.28 e Å−3 Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: 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 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810038936/hb5660sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810038936/hb5660Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H8N3+·C7H3N2O7F(000) = 696
Mr = 337.26Dx = 1.664 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2307 reflections
a = 9.1187 (4) Åθ = 2.4–28.6°
b = 11.3569 (5) ŵ = 0.14 mm1
c = 13.1343 (6) ÅT = 100 K
β = 98.204 (4)°Needle, yellow
V = 1346.27 (10) Å30.52 × 0.11 × 0.10 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer2785 independent reflections
Radiation source: fine-focus sealed tube1979 reflections with I > 2σ(I)
graphiteRint = 0.064
φ and ω scansθmax = 26.5°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −11→11
Tmin = 0.931, Tmax = 0.986k = −14→14
10195 measured reflectionsl = −16→16
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.070Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.162H-atom parameters constrained
S = 1.12w = 1/[σ2(Fo2) + (0.0439P)2 + 2.4565P] where P = (Fo2 + 2Fc2)/3
2785 reflections(Δ/σ)max < 0.001
279 parametersΔρmax = 0.46 e Å3
526 restraintsΔρmin = −0.28 e Å3
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.
xyzUiso*/UeqOcc. (<1)
N10.1346 (3)0.4299 (2)−0.0435 (2)0.0286 (7)
H1N10.22820.4863−0.02410.034*
N20.0269 (3)0.1468 (3)0.0541 (2)0.0370 (8)
H2N2−0.05500.10480.05730.044*
H1N20.10480.14170.11920.044*
N3−0.1784 (3)0.1759 (2)−0.1255 (2)0.0279 (7)
H1N3−0.17170.1109−0.08760.034*
H2N3−0.23760.1940−0.19420.034*
C10.1297 (4)0.3365 (3)0.0206 (3)0.0283 (8)
H1A0.19530.33250.08160.034*
C20.0275 (3)0.2469 (3)−0.0045 (3)0.0274 (8)
C3−0.0744 (3)0.2571 (3)−0.0968 (2)0.0253 (7)
C4−0.0643 (4)0.3579 (3)−0.1599 (3)0.0275 (8)
H4A−0.12990.3671−0.22040.033*
C50.0411 (4)0.4406 (3)−0.1315 (3)0.0298 (8)
H5A0.04860.5054−0.17370.036*
O10.3734 (3)0.5460 (2)0.06336 (19)0.0242 (7)0.886 (4)
O20.5011 (3)0.4686 (2)0.2297 (2)0.0278 (7)0.886 (4)
H20.44130.47770.17740.033*0.886 (4)
O30.6962 (5)0.5623 (2)0.3110 (3)0.0274 (9)0.886 (4)
O40.2470 (6)0.6533 (5)−0.1085 (5)0.0309 (11)0.886 (4)
O50.3768 (6)0.7848 (5)−0.1745 (3)0.0242 (10)0.886 (4)
O60.7238 (3)1.0170 (3)0.0450 (3)0.0246 (7)0.886 (4)
O70.8474 (3)0.9354 (3)0.1809 (2)0.0270 (7)0.886 (4)
N40.3541 (10)0.7207 (7)−0.1015 (5)0.0204 (9)0.886 (4)
N50.7468 (3)0.9350 (3)0.1074 (3)0.0191 (7)0.886 (4)
C60.5497 (8)0.8229 (5)0.0041 (4)0.0177 (14)0.886 (4)
H6A0.54420.8801−0.04700.021*0.886 (4)
C70.4568 (12)0.7259 (7)−0.0067 (6)0.0182 (12)0.886 (4)
C80.4606 (6)0.6350 (4)0.0699 (4)0.0179 (9)0.886 (4)
C90.5741 (4)0.6491 (3)0.1573 (3)0.0171 (8)0.886 (4)
C100.6650 (4)0.7456 (3)0.1681 (3)0.0162 (7)0.886 (4)
H10A0.73640.75300.22590.019*0.886 (4)
C110.6506 (5)0.8326 (4)0.0926 (3)0.0158 (8)0.886 (4)
C120.5956 (4)0.5570 (3)0.2394 (3)0.0210 (8)0.886 (4)
O1B0.703 (2)0.7054 (19)0.2650 (14)0.037 (6)*0.114 (4)
O2B0.598 (2)0.512 (2)0.2943 (15)0.034 (6)*0.114 (4)
H2B0.65840.56520.29560.01 (17)*0.114 (4)
O3B0.409 (3)0.4439 (19)0.1805 (19)0.051 (7)*0.114 (4)
O4B0.833 (2)0.892 (2)0.2101 (17)0.028 (6)*0.114 (4)
O5B0.722 (3)0.995 (2)0.0788 (19)0.013 (6)*0.114 (4)
O6B0.375 (7)0.811 (4)−0.176 (4)0.045 (16)*0.114 (4)
O7B0.250 (6)0.660 (5)−0.132 (4)0.044 (15)*0.114 (4)
N4B0.733 (3)0.908 (2)0.138 (2)0.032 (7)*0.114 (4)
N5B0.353 (10)0.733 (7)−0.115 (4)0.032 (7)*0.114 (4)
C6B0.537 (6)0.824 (4)0.018 (3)0.011 (6)*0.114 (4)
H6BA0.53620.8931−0.02000.013*0.114 (4)
C7B0.633 (4)0.811 (3)0.110 (2)0.011 (6)*0.114 (4)
C8B0.620 (3)0.714 (2)0.1781 (16)0.007 (6)*0.114 (4)
C9B0.520 (3)0.6226 (19)0.1401 (17)0.014 (5)*0.114 (4)
C10B0.432 (5)0.633 (3)0.049 (3)0.014 (5)*0.114 (4)
H10B0.36390.57460.02750.016*0.114 (4)
C11B0.442 (12)0.732 (7)−0.014 (5)0.026 (6)*0.114 (4)
C12B0.499 (3)0.521 (2)0.2106 (18)0.026 (6)*0.114 (4)
U11U22U33U12U13U23
N10.0268 (15)0.0294 (15)0.0305 (16)0.0010 (13)0.0071 (13)−0.0046 (12)
N20.0307 (15)0.0329 (17)0.0469 (19)−0.0038 (14)0.0036 (14)0.0063 (14)
N30.0288 (14)0.0247 (14)0.0296 (15)−0.0042 (12)0.0017 (12)0.0005 (12)
C10.0268 (17)0.0239 (17)0.037 (2)0.0027 (15)0.0138 (15)−0.0011 (15)
C20.0254 (17)0.0312 (18)0.0262 (17)0.0103 (15)0.0055 (14)−0.0011 (14)
C30.0219 (16)0.0277 (18)0.0282 (18)0.0005 (14)0.0098 (14)−0.0089 (14)
C40.0260 (16)0.0239 (17)0.0346 (19)0.0016 (14)0.0110 (15)−0.0036 (14)
C50.0318 (18)0.0268 (18)0.0319 (19)0.0035 (15)0.0089 (15)0.0015 (14)
O10.0243 (13)0.0203 (13)0.0282 (14)−0.0050 (11)0.0047 (11)−0.0006 (10)
O20.0340 (15)0.0211 (15)0.0283 (15)−0.0031 (12)0.0053 (12)0.0083 (12)
O30.0300 (15)0.0260 (19)0.0258 (16)0.0037 (12)0.0021 (15)0.0078 (11)
O40.0240 (18)0.034 (2)0.033 (3)−0.0167 (12)−0.0016 (18)0.0034 (19)
O50.0281 (19)0.024 (2)0.0201 (18)−0.0091 (18)0.0016 (11)0.0047 (15)
O60.0303 (16)0.0173 (15)0.0266 (18)−0.0026 (11)0.0051 (14)0.0060 (13)
O70.0245 (14)0.0227 (15)0.0308 (16)−0.0050 (12)−0.0065 (12)−0.0017 (13)
N40.0193 (16)0.023 (3)0.020 (2)−0.0003 (18)0.0050 (17)−0.0003 (14)
N50.0198 (16)0.0176 (18)0.0203 (18)0.0005 (14)0.0038 (14)−0.0027 (15)
C60.019 (2)0.0193 (19)0.016 (2)0.0018 (15)0.009 (2)−0.0020 (16)
C70.016 (3)0.020 (2)0.020 (2)0.002 (2)0.0068 (14)−0.0020 (14)
C80.018 (3)0.0159 (17)0.021 (3)0.0011 (16)0.0086 (17)−0.0020 (16)
C90.018 (2)0.0158 (18)0.0183 (17)0.0026 (16)0.0059 (14)0.0005 (14)
C100.0153 (17)0.0164 (18)0.0182 (18)−0.0011 (16)0.0067 (14)−0.0041 (14)
C110.018 (2)0.011 (2)0.020 (2)−0.0012 (14)0.0103 (16)−0.0006 (14)
C120.0255 (19)0.0153 (16)0.024 (2)0.0030 (15)0.0096 (16)0.0010 (15)
N1—C51.341 (4)C6—C71.384 (5)
N1—C11.358 (4)C6—H6A0.9300
N1—H1N11.0684C7—C81.438 (5)
N2—C21.373 (4)C8—C91.441 (5)
N2—H2N20.8919C9—C101.369 (5)
N2—H1N21.0329C9—C121.494 (5)
N3—C31.338 (4)C10—C111.393 (5)
N3—H1N30.8875C10—H10A0.9300
N3—H2N31.0043O1B—C8B1.281 (16)
C1—C21.387 (5)O2B—C12B1.322 (16)
C1—H1A0.9300O2B—H2B0.8200
C2—C31.423 (4)O3B—C12B1.229 (17)
C3—C41.424 (5)O4B—N4B1.230 (17)
C4—C51.357 (5)O5B—N4B1.249 (17)
C4—H4A0.9300O6B—N5B1.237 (18)
C5—H5A0.9300O7B—N5B1.246 (18)
O1—C81.282 (5)N4B—C7B1.445 (16)
O2—C121.317 (4)N5B—C11B1.454 (17)
O2—H20.8200C6B—C11B1.386 (18)
O3—C121.219 (6)C6B—C7B1.388 (18)
O4—N41.234 (4)C6B—H6BA0.9300
O5—N41.244 (5)C7B—C8B1.436 (16)
O6—N51.239 (5)C8B—C9B1.424 (16)
O7—N51.233 (4)C9B—C10B1.348 (16)
N4—C71.449 (5)C9B—C12B1.507 (16)
N5—C111.453 (5)C10B—C11B1.398 (18)
C6—C111.381 (5)C10B—H10B0.9300
C5—N1—C1122.1 (3)C10—C9—C8121.8 (3)
C5—N1—H1N1122.6C10—C9—C12118.0 (3)
C1—N1—H1N1114.6C8—C9—C12120.2 (3)
C2—N2—H2N2122.6C9—C10—C11120.0 (3)
C2—N2—H1N2116.9C9—C10—H10A120.0
H2N2—N2—H1N2114.3C11—C10—H10A120.0
C3—N3—H1N3115.2C6—C11—C10121.8 (4)
C3—N3—H2N3112.3C6—C11—N5119.6 (4)
H1N3—N3—H2N3131.3C10—C11—N5118.6 (3)
N1—C1—C2120.4 (3)O3—C12—O2121.5 (3)
N1—C1—H1A119.8O3—C12—C9122.0 (3)
C2—C1—H1A119.8O2—C12—C9116.5 (3)
N2—C2—C1122.0 (3)C12B—O2B—H2B109.5
N2—C2—C3119.4 (3)O4B—N4B—O5B126 (2)
C1—C2—C3118.5 (3)O4B—N4B—C7B116.9 (19)
N3—C3—C2122.3 (3)O5B—N4B—C7B116.5 (18)
N3—C3—C4119.5 (3)O6B—N5B—O7B123 (3)
C2—C3—C4118.3 (3)O6B—N5B—C11B119 (2)
C5—C4—C3119.9 (3)O7B—N5B—C11B118 (3)
C5—C4—H4A120.1C11B—C6B—C7B118.0 (19)
C3—C4—H4A120.1C11B—C6B—H6BA121.0
N1—C5—C4120.8 (3)C7B—C6B—H6BA121.0
N1—C5—H5A119.6C6B—C7B—C8B121.6 (17)
C4—C5—H5A119.6C6B—C7B—N4B115.9 (18)
C12—O2—H2109.5C8B—C7B—N4B121.9 (17)
O4—N4—O5121.5 (4)O1B—C8B—C9B121.6 (16)
O4—N4—C7119.8 (4)O1B—C8B—C7B121.6 (17)
O5—N4—C7118.7 (4)C9B—C8B—C7B116.4 (15)
O7—N5—O6123.5 (3)C10B—C9B—C8B120.9 (16)
O7—N5—C11118.3 (4)C10B—C9B—C12B120.2 (17)
O6—N5—C11118.1 (3)C8B—C9B—C12B118.2 (15)
C11—C6—C7118.3 (4)C9B—C10B—C11B121 (2)
C11—C6—H6A120.9C9B—C10B—H10B119.5
C7—C6—H6A120.9C11B—C10B—H10B119.5
C6—C7—C8123.1 (4)C6B—C11B—C10B121.0 (19)
C6—C7—N4115.5 (4)C6B—C11B—N5B121 (2)
C8—C7—N4121.3 (4)C10B—C11B—N5B118 (2)
O1—C8—C7124.5 (4)O3B—C12B—O2B124 (2)
O1—C8—C9120.6 (4)O3B—C12B—C9B119.1 (17)
C7—C8—C9114.9 (3)O2B—C12B—C9B116.2 (17)
C5—N1—C1—C21.0 (5)O6—N5—C11—C10−173.2 (4)
N1—C1—C2—N2174.7 (3)C10—C9—C12—O3−4.5 (5)
N1—C1—C2—C3−1.9 (5)C8—C9—C12—O3175.3 (4)
N2—C2—C3—N34.7 (5)C10—C9—C12—O2176.3 (3)
C1—C2—C3—N3−178.6 (3)C8—C9—C12—O2−3.8 (5)
N2—C2—C3—C4−175.5 (3)C11B—C6B—C7B—C8B−10 (11)
C1—C2—C3—C41.2 (4)C11B—C6B—C7B—N4B178 (8)
N3—C3—C4—C5−179.8 (3)O4B—N4B—C7B—C6B−170 (5)
C2—C3—C4—C50.4 (5)O5B—N4B—C7B—C6B1(7)
C1—N1—C5—C40.7 (5)O4B—N4B—C7B—C8B18 (6)
C3—C4—C5—N1−1.4 (5)O5B—N4B—C7B—C8B−171 (4)
C11—C6—C7—C80.0 (17)C6B—C7B—C8B—O1B−176 (5)
C11—C6—C7—N4−179.7 (9)N4B—C7B—C8B—O1B−5(6)
O4—N4—C7—C6−164.1 (11)C6B—C7B—C8B—C9B10 (7)
O5—N4—C7—C616.1 (17)N4B—C7B—C8B—C9B−179 (4)
O4—N4—C7—C816.2 (18)O1B—C8B—C9B—C10B179 (4)
O5—N4—C7—C8−163.6 (11)C7B—C8B—C9B—C10B−7(6)
C6—C7—C8—O1178.0 (9)O1B—C8B—C9B—C12B8(5)
N4—C7—C8—O1−2.3 (17)C7B—C8B—C9B—C12B−178 (3)
C6—C7—C8—C9−3.0 (16)C8B—C9B—C10B—C11B4(10)
N4—C7—C8—C9176.7 (10)C12B—C9B—C10B—C11B175 (8)
O1—C8—C9—C10−177.5 (4)C7B—C6B—C11B—C10B7(16)
C7—C8—C9—C103.5 (9)C7B—C6B—C11B—N5B−172 (10)
O1—C8—C9—C122.7 (7)C9B—C10B—C11B—C6B−4(16)
C7—C8—C9—C12−176.4 (7)C9B—C10B—C11B—N5B175 (9)
C8—C9—C10—C11−1.0 (6)O6B—N5B—C11B—C6B9(19)
C12—C9—C10—C11178.9 (4)O7B—N5B—C11B—C6B−167 (12)
C7—C6—C11—C102.8 (12)O6B—N5B—C11B—C10B−170 (11)
C7—C6—C11—N5−178.3 (9)O7B—N5B—C11B—C10B15 (18)
C9—C10—C11—C6−2.3 (7)C10B—C9B—C12B—O3B6(6)
C9—C10—C11—N5178.7 (4)C8B—C9B—C12B—O3B177 (3)
O7—N5—C11—C6−171.6 (5)C10B—C9B—C12B—O2B175 (4)
O6—N5—C11—C67.8 (7)C8B—C9B—C12B—O2B−14 (4)
O7—N5—C11—C107.3 (6)
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O11.071.762.753 (4)153
O2—H2···O10.821.722.485 (4)154
N2—H2N2···O6i0.892.243.120 (4)171
N2—H1N2···O3ii1.032.113.026 (5)146
N3—H1N3···O6i0.892.363.104 (4)142
N3—H2N3···O5iii1.002.243.217 (5)163
C6—H6A···O3iv0.932.563.299 (6)136
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1N1⋯O11.071.762.753 (4)153
N2—H2N2⋯O6i0.892.243.120 (4)171
N2—H1N2⋯O3ii1.032.113.026 (5)146
N3—H1N3⋯O6i0.892.363.104 (4)142
N3—H2N3⋯O5iii1.002.243.217 (5)163
C6—H6A⋯O3iv0.932.563.299 (6)136

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

  2 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  2 in total

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