Literature DB >> 22259412

2-Amino-pyridinium 2-meth-oxy-carbonyl-4,6-dinitro-phenolate.

Dong-Liang Wu1, Zi-Jing Xiao.   

Abstract

In the title mol-ecular salt, C(5)H(7)N(2) (+)·C(8)H(5)N(2)O(7) (-), the 2-amino-pyridinium cation is essentially planar, with a maximium deviation of 0.015 (1) Å, while the 2-meth-oxy-carbonyl-4,6-dinitro-phenolate anion is slightly twisted away from planarity, with a maximium deviation of 0.187 (1) Å. Deprotonation of the hy-droxy O atom was observed. The cation and anion are connected by four bifurcated N-H⋯(O,O) hydrogen bonds, forming a mol-ecular proton-transfer adduct. The dihedral angle between the pyridinium ring in the cation and the benzene ring in the anion is 3.65 (6)°. Every adduct connects to six neighboring adducts by N-H⋯O and C-H⋯O hydrogen bonds, yielding extended layers parallel to the bc plane. There is a weak π-π inter-action between the benzene rings of two neighboring anions; the inter-planar spacing and the centroid-centroid separation are 3.309 (1) and 3.69 (1) Å, respectively.

Entities:  

Year:  2011        PMID: 22259412      PMCID: PMC3254471          DOI: 10.1107/S160053681105286X

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


Related literature

For the structures of mol­ecular proton-transfer adducts containing substituted pyridinium and an acid anion, see Gellert & Hsu (1988 ▶); Smith et al. (2000 ▶); Jebas et al. (2006 ▶); Rademeyer (2007 ▶); Hemamalini & Fun (2010a ▶,b ▶,c ▶); Perpétuo & Janczak (2010 ▶). For comparable structures, see: Jebas et al. (2006 ▶); Perpétuo & Janczak (2010 ▶); Hemamalini & Fun (2010a ▶). For the synthesis of 3,5-dinitro­methyl salicylate, see: Bartlett & Trachten (1958 ▶).

Experimental

Crystal data

C5H7N2 +·C8H5N2O7 − M = 336.27 Monoclinic, a = 7.4088 (3) Å b = 19.1779 (6) Å c = 9.9784 (4) Å β = 98.2825 (15)° V = 1403.00 (9) Å3 Z = 4 Mo Kα radiation μ = 0.13 mm−1 T = 293 K 0.35 × 0.35 × 0.26 mm

Data collection

Rigaku R-AXIS SPIDER IP diffractometer Absorption correction: ψ scan (TEXRAY; Molecular Structure Corporation, 1999) ▶ T min = 0.951, T max = 0.969 21789 measured reflections 3200 independent reflections 2760 reflections with I > 2σ(I) R int = 0.024

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.111 S = 1.09 3200 reflections 221 parameters H-atom parameters constrained Δρmax = 0.32 e Å−3 Δρmin = −0.30 e Å−3 Data collection: RAPID-AUTO (Rigaku, 2008 ▶); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEX (McArdle, 1995 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S160053681105286X/ez2268sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681105286X/ez2268Isup2.hkl Supplementary material file. DOI: 10.1107/S160053681105286X/ez2268Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H7N2+·C8H5N2O7F(000) = 696
Mr = 336.27Dx = 1.592 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3200 reflections
a = 7.4088 (3) Åθ = 3.2–27.5°
b = 19.1779 (6) ŵ = 0.13 mm1
c = 9.9784 (4) ÅT = 293 K
β = 98.2825 (15)°Block, pale yellow
V = 1403.00 (9) Å30.35 × 0.35 × 0.26 mm
Z = 4
Rigaku R-AXIS SPIDER IP diffractometer3200 independent reflections
Radiation source: fine-focus sealed tube2760 reflections with I > 2σ(I)
graphiteRint = 0.024
φ and ω scanθmax = 27.5°, θmin = 3.2°
Absorption correction: ψ scan (TEXRAY; Molecular Structure Corporation, 1999)h = −9→9
Tmin = 0.951, Tmax = 0.969k = −24→24
21789 measured reflectionsl = −12→12
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.111H-atom parameters constrained
S = 1.09w = 1/[σ2(Fo2) + (0.0608P)2 + 0.3452P] where P = (Fo2 + 2Fc2)/3
3200 reflections(Δ/σ)max = 0.001
221 parametersΔρmax = 0.32 e Å3
0 restraintsΔρmin = −0.30 e Å3
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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*/Ueq
C1−0.02842 (16)0.69774 (6)0.60013 (13)0.0241 (3)
C2−0.11062 (17)0.75222 (6)0.66522 (14)0.0289 (3)
H2A−0.16390.78970.61510.035*
C3−0.11154 (18)0.74967 (7)0.80192 (14)0.0311 (3)
H3A−0.16570.78560.84450.037*
C4−0.03148 (18)0.69327 (7)0.87924 (13)0.0307 (3)
H4A−0.02990.69190.97260.037*
C50.04326 (17)0.64096 (7)0.81366 (12)0.0267 (3)
H5A0.09520.60290.86250.032*
C60.29417 (15)0.45835 (6)0.52321 (11)0.0210 (2)
C70.22285 (16)0.51541 (6)0.43454 (12)0.0222 (2)
C80.25155 (16)0.50645 (6)0.29470 (12)0.0228 (2)
C90.34193 (16)0.45058 (6)0.24919 (11)0.0232 (2)
H9A0.35710.44730.15850.028*
C100.41023 (15)0.39918 (6)0.34032 (12)0.0215 (2)
C110.38567 (16)0.40290 (6)0.47609 (12)0.0214 (2)
H11A0.43140.36760.53550.026*
C120.27237 (16)0.46104 (6)0.66889 (12)0.0237 (2)
C130.3255 (2)0.40100 (9)0.87787 (14)0.0451 (4)
H13A0.33990.35380.90980.068*
H13B0.20930.41850.89420.068*
H13C0.42090.42940.92500.068*
N10.04300 (14)0.64367 (5)0.67753 (10)0.0233 (2)
H01A0.08710.60720.63660.044 (5)*
N2−0.01983 (16)0.69663 (6)0.46755 (11)0.0301 (3)
H02A0.02120.65920.42980.043 (5)*
H02B−0.05600.73300.41890.043 (5)*
N30.18614 (16)0.55870 (6)0.19326 (11)0.0312 (3)
N40.50832 (14)0.34132 (5)0.29295 (10)0.0241 (2)
O10.33525 (16)0.40289 (5)0.73434 (9)0.0380 (3)
O20.20907 (15)0.50859 (5)0.72572 (9)0.0361 (2)
O30.14378 (14)0.56716 (5)0.47530 (9)0.0347 (2)
O40.12739 (17)0.61428 (5)0.22518 (11)0.0425 (3)
O50.1928 (3)0.54493 (9)0.07588 (12)0.1015 (8)
O60.52421 (14)0.33865 (5)0.17125 (9)0.0329 (2)
O70.57286 (14)0.29666 (5)0.37464 (10)0.0342 (2)
U11U22U33U12U13U23
C10.0235 (5)0.0210 (5)0.0277 (6)−0.0042 (4)0.0030 (5)0.0003 (4)
C20.0288 (6)0.0210 (6)0.0366 (7)0.0003 (5)0.0031 (5)−0.0011 (5)
C30.0305 (6)0.0267 (6)0.0367 (7)−0.0006 (5)0.0073 (5)−0.0103 (5)
C40.0331 (7)0.0338 (7)0.0255 (6)−0.0029 (5)0.0057 (5)−0.0063 (5)
C50.0288 (6)0.0273 (6)0.0237 (6)−0.0016 (5)0.0028 (5)−0.0001 (5)
C60.0221 (5)0.0229 (6)0.0181 (5)−0.0014 (4)0.0027 (4)−0.0004 (4)
C70.0239 (5)0.0221 (5)0.0206 (5)0.0005 (4)0.0029 (4)−0.0010 (4)
C80.0257 (6)0.0229 (6)0.0194 (5)−0.0001 (4)0.0014 (4)0.0028 (4)
C90.0258 (6)0.0264 (6)0.0175 (5)−0.0016 (4)0.0034 (4)−0.0008 (4)
C100.0226 (5)0.0203 (5)0.0219 (6)−0.0007 (4)0.0046 (4)−0.0027 (4)
C110.0225 (5)0.0210 (5)0.0206 (5)−0.0017 (4)0.0028 (4)0.0012 (4)
C120.0248 (6)0.0258 (6)0.0206 (5)0.0007 (4)0.0034 (4)0.0004 (4)
C130.0604 (10)0.0566 (10)0.0200 (7)0.0201 (8)0.0117 (6)0.0107 (6)
N10.0261 (5)0.0209 (5)0.0233 (5)0.0003 (4)0.0053 (4)−0.0014 (4)
N20.0410 (6)0.0236 (5)0.0261 (5)0.0033 (4)0.0062 (5)0.0037 (4)
N30.0399 (6)0.0313 (6)0.0224 (5)0.0076 (5)0.0046 (5)0.0052 (4)
N40.0256 (5)0.0230 (5)0.0244 (5)−0.0013 (4)0.0061 (4)−0.0022 (4)
O10.0586 (7)0.0379 (5)0.0194 (4)0.0191 (5)0.0117 (4)0.0066 (4)
O20.0546 (6)0.0321 (5)0.0237 (4)0.0117 (4)0.0125 (4)−0.0005 (4)
O30.0507 (6)0.0296 (5)0.0246 (5)0.0156 (4)0.0084 (4)0.0011 (4)
O40.0678 (7)0.0245 (5)0.0355 (5)0.0100 (5)0.0088 (5)0.0069 (4)
O50.1943 (19)0.0906 (11)0.0208 (6)0.0938 (13)0.0190 (8)0.0151 (6)
O60.0432 (5)0.0334 (5)0.0237 (4)0.0050 (4)0.0097 (4)−0.0060 (4)
O70.0433 (5)0.0269 (5)0.0340 (5)0.0102 (4)0.0117 (4)0.0055 (4)
C1—N21.3338 (16)C9—C101.3864 (16)
C1—N11.3543 (16)C9—H9A0.9300
C1—C21.4136 (17)C10—C111.3945 (15)
C2—C31.3659 (19)C10—N41.4429 (15)
C2—H2A0.9300C11—H11A0.9300
C3—C41.409 (2)C12—O21.2041 (15)
C3—H3A0.9300C12—O11.3414 (15)
C4—C51.3586 (18)C13—O11.4448 (15)
C4—H4A0.9300C13—H13A0.9600
C5—N11.3591 (15)C13—H13B0.9600
C5—H5A0.9300C13—H13C0.9600
C6—C111.3796 (16)N1—H01A0.8952
C6—C71.4578 (16)N2—H02A0.8838
C6—C121.4864 (15)N2—H02B0.8702
C7—O31.2498 (14)N3—O51.2087 (16)
C7—C81.4516 (16)N3—O41.2112 (15)
C8—C91.3748 (17)N4—O71.2307 (14)
C8—N31.4568 (15)N4—O61.2378 (13)
N2—C1—N1118.87 (11)C9—C10—N4119.04 (10)
N2—C1—C2123.56 (11)C11—C10—N4119.99 (10)
N1—C1—C2117.56 (11)C6—C11—C10120.65 (10)
C3—C2—C1119.79 (12)C6—C11—H11A119.7
C3—C2—H2A120.1C10—C11—H11A119.7
C1—C2—H2A120.1O2—C12—O1122.13 (11)
C2—C3—C4120.81 (12)O2—C12—C6126.26 (11)
C2—C3—H3A119.6O1—C12—C6111.61 (10)
C4—C3—H3A119.6O1—C13—H13A109.5
C5—C4—C3118.15 (12)O1—C13—H13B109.5
C5—C4—H4A120.9H13A—C13—H13B109.5
C3—C4—H4A120.9O1—C13—H13C109.5
C4—C5—N1120.74 (12)H13A—C13—H13C109.5
C4—C5—H5A119.6H13B—C13—H13C109.5
N1—C5—H5A119.6C1—N1—C5122.92 (10)
C11—C6—C7121.65 (10)C1—N1—H01A118.4
C11—C6—C12119.21 (10)C5—N1—H01A118.6
C7—C6—C12119.11 (10)C1—N2—H02A120.2
O3—C7—C8123.18 (11)C1—N2—H02B119.0
O3—C7—C6122.99 (10)H02A—N2—H02B120.7
C8—C7—C6113.83 (10)O5—N3—O4120.90 (12)
C9—C8—C7123.75 (10)O5—N3—C8117.84 (11)
C9—C8—N3115.83 (10)O4—N3—C8121.25 (11)
C7—C8—N3120.41 (10)O7—N4—O6122.57 (10)
C8—C9—C10119.11 (10)O7—N4—C10118.96 (10)
C8—C9—H9A120.4O6—N4—C10118.47 (10)
C10—C9—H9A120.4C12—O1—C13116.11 (10)
C9—C10—C11120.97 (10)
N2—C1—C2—C3−179.20 (12)C9—C10—C11—C6−0.67 (17)
N1—C1—C2—C31.62 (18)N4—C10—C11—C6179.18 (10)
C1—C2—C3—C4−0.03 (19)C11—C6—C12—O2173.68 (12)
C2—C3—C4—C5−1.28 (19)C7—C6—C12—O2−4.57 (18)
C3—C4—C5—N10.98 (19)C11—C6—C12—O1−5.50 (16)
C11—C6—C7—O3−178.03 (11)C7—C6—C12—O1176.25 (10)
C12—C6—C7—O30.17 (18)N2—C1—N1—C5178.80 (11)
C11—C6—C7—C82.18 (16)C2—C1—N1—C5−1.97 (17)
C12—C6—C7—C8−179.61 (10)C4—C5—N1—C10.68 (18)
O3—C7—C8—C9178.46 (12)C9—C8—N3—O510.0 (2)
C6—C7—C8—C9−1.76 (17)C7—C8—N3—O5−170.96 (17)
O3—C7—C8—N3−0.49 (18)C9—C8—N3—O4−169.76 (12)
C6—C7—C8—N3179.30 (10)C7—C8—N3—O49.27 (19)
C7—C8—C9—C100.18 (18)C9—C10—N4—O7178.17 (11)
N3—C8—C9—C10179.17 (10)C11—C10—N4—O7−1.68 (16)
C8—C9—C10—C111.12 (17)C9—C10—N4—O6−1.80 (16)
C8—C9—C10—N4−178.74 (10)C11—C10—N4—O6178.35 (10)
C7—C6—C11—C10−1.09 (17)O2—C12—O1—C13−1.0 (2)
C12—C6—C11—C10−179.29 (10)C6—C12—O1—C13178.21 (12)
D—H···AD—HH···AD···AD—H···A
N1—H01A···O30.901.882.6864 (13)148.
N1—H01A···O20.902.232.8783 (14)130.
N2—H02A···O30.882.012.7592 (14)142.
N2—H02A···O40.882.453.2082 (15)144.
N2—H02B···O6i0.872.243.0537 (14)155.
C4—H4A···O7ii0.932.573.2052 (16)126.
C5—H5A···O5iii0.932.423.2604 (17)151.
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H01A⋯O30.901.882.6864 (13)148
N1—H01A⋯O20.902.232.8783 (14)130
N2—H02A⋯O30.882.012.7592 (14)142
N2—H02A⋯O40.882.453.2082 (15)144
N2—H02B⋯O6i0.872.243.0537 (14)155
C4—H4A⋯O7ii0.932.573.2052 (16)126
C5—H5A⋯O5iii0.932.423.2604 (17)151

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

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2.  A short history of SHELX.

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3.  Hydrogen-bonded networks in 5-chloropyridin-2-amine-fumaric acid (2/1) and 2-aminopyridinium DL-malate.

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4.  2-Aminopyridinium salicylate.

Authors:  R W Gellert; I N Hsu
Journal:  Acta Crystallogr C       Date:  1988-02-15       Impact factor: 1.172

5.  2-Amino-pyridinium trifluoro-acetate.

Authors:  Madhukar Hemamalini; Hoong-Kun Fun
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6.  2-Amino-5-chloro-pyridinium salicylate.

Authors:  Madhukar Hemamalini; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-05-22

7.  2-Amino-5-chloro-pyridinium 3-carb-oxy-4-hy-droxy-benzene-sulfonate.

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