Literature DB >> 21582810

2,3-Diamino-pyridinium benzoate.

Kasthuri Balasubramani1, Hoong-Kun Fun.   

Abstract

In the title compound, C(5)H(8)N(3) (+)·C(7)H(5)O(2) (-), the n class="Chemical">pyridine N atom is protonated. The carboxyl-ate group of the benzoate anion is twisted away from the attached ring by 10.91 (9)°. In the crystal structure, N-H⋯O hydrogen bonds between 2,3-diamino-pyridinium cations and benzoate anions, and π-π inter-actions between the pyridinium rings [centroid-centroid distance = 3.6467 (9) Å] form a two-dimensional network parallel to (001). In the network, N-H⋯O hydrogen bonds form R(2) (2)(8) and R(2) (1)(7) ring motifs.

Entities:  

Year:  2009        PMID: 21582810      PMCID: PMC2969407          DOI: 10.1107/S1600536809021011

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


Related literature

For general background to pyridine derivatives, see: Pozharski et al. (1997 ▶); Katritzky et al. (1996 ▶). For bond-length data, see: Allen et al. (1987 ▶). For details of n class="Chemical">hydrogen bonding, see: Jeffrey & Saenger (1991 ▶); Jeffrey (1997 ▶); Scheiner (1997 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C5H8N3C7H5O2 M = 231.25 Orthorhombic, a = 10.1498 (3) Å b = 11.0656 (3) Å c = 20.7368 (7) Å V = 2329.03 (12) Å3 Z = 8 Mo Kα radiation μ = 0.09 mm−1 T = 100 K 0.43 × 0.40 × 0.03 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2005 ▶) T min = 0.935, T max = 0.998 27109 measured reflections 3443 independent reflections 2559 reflections with I > 2σ(I) R int = 0.070

Refinement

R[F 2 > 2σ(F 2)] = 0.065 wR(F 2) = 0.124 S = 1.09 3443 reflections 206 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.26 e Å−3 Δρmin = −0.22 e Å−3 Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); 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/S1600536809021011/ci2821sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809021011/ci2821Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H8N3+·C7H5O2F(000) = 976
Mr = 231.25Dx = 1.319 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 3782 reflections
a = 10.1498 (3) Åθ = 2.8–27.9°
b = 11.0656 (3) ŵ = 0.09 mm1
c = 20.7368 (7) ÅT = 100 K
V = 2329.03 (12) Å3Plate, brown
Z = 80.43 × 0.40 × 0.03 mm
Bruker SMART APEXII CCD area-detector diffractometer3443 independent reflections
Radiation source: fine-focus sealed tube2559 reflections with I > 2σ(I)
graphiteRint = 0.070
φ and ω scansθmax = 30.1°, θmin = 2.9°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −14→14
Tmin = 0.935, Tmax = 0.998k = −15→15
27109 measured reflectionsl = −26→29
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.065Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.124H atoms treated by a mixture of independent and constrained refinement
S = 1.09w = 1/[σ2(Fo2) + (0.0394P)2 + 1.0527P] where P = (Fo2 + 2Fc2)/3
3443 reflections(Δ/σ)max = 0.001
206 parametersΔρmax = 0.26 e Å3
0 restraintsΔρmin = −0.22 e Å3
Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
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.
xyzUiso*/Ueq
O10.41320 (11)0.39789 (9)0.63510 (5)0.0253 (3)
O20.39681 (11)0.57595 (9)0.58541 (5)0.0257 (3)
C60.54129 (15)0.55976 (13)0.67572 (8)0.0217 (3)
C10.57778 (16)0.49395 (15)0.73019 (8)0.0271 (4)
C20.66687 (18)0.54115 (17)0.77390 (10)0.0347 (4)
C30.72160 (19)0.65474 (16)0.76378 (10)0.0365 (4)
C40.68658 (19)0.72004 (16)0.70966 (10)0.0375 (5)
C50.59687 (17)0.67368 (14)0.66578 (9)0.0296 (4)
C70.44423 (15)0.50698 (13)0.62917 (7)0.0211 (3)
C90.06661 (15)0.32936 (13)0.46855 (8)0.0220 (3)
C80.15562 (15)0.37759 (13)0.51515 (8)0.0211 (3)
N10.22115 (13)0.47997 (11)0.50049 (7)0.0230 (3)
N20.17608 (14)0.32713 (12)0.57320 (7)0.0239 (3)
N3−0.00614 (14)0.22766 (12)0.48334 (8)0.0273 (3)
C120.20715 (17)0.53936 (14)0.44310 (9)0.0270 (4)
C110.12491 (17)0.49519 (15)0.39762 (9)0.0288 (4)
C100.05443 (17)0.38821 (14)0.41056 (9)0.0268 (4)
H12A0.262 (2)0.6122 (17)0.4384 (9)0.039 (5)*
H11A0.1152 (17)0.5333 (16)0.3555 (9)0.028 (5)*
H10A−0.0033 (18)0.3556 (15)0.3778 (9)0.027 (5)*
H1A0.5401 (19)0.4138 (17)0.7363 (9)0.037 (5)*
H2A0.690 (2)0.4955 (18)0.8134 (10)0.045 (6)*
H3A0.785 (2)0.6890 (17)0.7969 (10)0.043 (6)*
H4A0.726 (2)0.7970 (19)0.7013 (10)0.051 (6)*
H5A0.5737 (18)0.7200 (17)0.6276 (9)0.032 (5)*
H1N10.283 (2)0.5096 (18)0.5312 (9)0.039 (5)*
H1N20.248 (2)0.3487 (16)0.5959 (9)0.033 (5)*
H2N20.146 (2)0.253 (2)0.5800 (10)0.047 (6)*
H1N30.021 (2)0.1812 (18)0.5170 (10)0.042 (6)*
H2N3−0.043 (2)0.1882 (17)0.4469 (10)0.041 (6)*
U11U22U33U12U13U23
O10.0278 (6)0.0181 (5)0.0298 (6)−0.0009 (4)−0.0021 (5)0.0002 (4)
O20.0280 (6)0.0205 (5)0.0285 (6)−0.0020 (4)−0.0058 (5)0.0020 (4)
C60.0181 (7)0.0209 (7)0.0261 (8)0.0037 (5)0.0001 (6)−0.0025 (6)
C10.0252 (8)0.0271 (8)0.0291 (9)0.0039 (6)−0.0009 (7)0.0015 (7)
C20.0335 (10)0.0398 (10)0.0308 (10)0.0067 (8)−0.0089 (8)0.0007 (8)
C30.0339 (10)0.0346 (9)0.0410 (11)0.0058 (7)−0.0150 (8)−0.0104 (8)
C40.0361 (10)0.0245 (8)0.0520 (12)−0.0009 (7)−0.0165 (9)−0.0026 (8)
C50.0298 (9)0.0227 (7)0.0364 (10)0.0003 (6)−0.0111 (8)0.0019 (7)
C70.0197 (7)0.0210 (7)0.0226 (8)0.0019 (5)0.0027 (6)−0.0013 (6)
C90.0194 (7)0.0182 (7)0.0285 (9)0.0017 (5)−0.0004 (6)−0.0027 (6)
C80.0192 (7)0.0175 (6)0.0265 (8)0.0028 (5)0.0011 (6)−0.0016 (6)
N10.0223 (7)0.0186 (6)0.0281 (7)−0.0011 (5)−0.0013 (6)−0.0012 (5)
N20.0237 (7)0.0213 (6)0.0269 (8)−0.0029 (5)−0.0020 (6)0.0014 (5)
N30.0288 (7)0.0217 (6)0.0314 (8)−0.0048 (5)−0.0055 (7)0.0010 (6)
C120.0286 (9)0.0204 (7)0.0320 (9)−0.0014 (6)0.0008 (7)0.0038 (6)
C110.0319 (9)0.0260 (8)0.0285 (9)0.0006 (7)−0.0019 (7)0.0054 (7)
C100.0252 (8)0.0269 (8)0.0283 (9)0.0000 (6)−0.0043 (7)−0.0014 (7)
O1—C71.2537 (17)C9—N31.3805 (19)
O2—C71.2796 (18)C9—C81.427 (2)
C6—C11.394 (2)C8—N21.343 (2)
C6—C51.396 (2)C8—N11.3484 (19)
C6—C71.498 (2)N1—C121.367 (2)
C1—C21.383 (2)N1—H1N10.96 (2)
C1—H1A0.974 (19)N2—H1N20.90 (2)
C2—C31.390 (3)N2—H2N20.88 (2)
C2—H2A0.99 (2)N3—H1N30.91 (2)
C3—C41.381 (3)N3—H2N30.95 (2)
C3—H3A1.02 (2)C12—C111.351 (2)
C4—C51.386 (2)C12—H12A0.99 (2)
C4—H4A0.96 (2)C11—C101.409 (2)
C5—H5A0.972 (19)C11—H11A0.975 (18)
C9—C101.373 (2)C10—H10A0.966 (18)
C1—C6—C5118.94 (15)N3—C9—C8119.55 (15)
C1—C6—C7119.56 (14)N2—C8—N1118.36 (14)
C5—C6—C7121.50 (14)N2—C8—C9123.34 (14)
C2—C1—C6120.50 (16)N1—C8—C9118.29 (14)
C2—C1—H1A121.0 (12)C8—N1—C12123.30 (14)
C6—C1—H1A118.5 (12)C8—N1—H1N1117.7 (12)
C1—C2—C3120.25 (17)C12—N1—H1N1119.0 (12)
C1—C2—H2A120.4 (12)C8—N2—H1N2118.9 (12)
C3—C2—H2A119.3 (12)C8—N2—H2N2118.3 (14)
C4—C3—C2119.53 (17)H1N2—N2—H2N2116.3 (18)
C4—C3—H3A121.2 (11)C9—N3—H1N3117.9 (13)
C2—C3—H3A119.3 (11)C9—N3—H2N3114.0 (12)
C3—C4—C5120.59 (17)H1N3—N3—H2N3118.1 (17)
C3—C4—H4A120.4 (13)C11—C12—N1119.87 (15)
C5—C4—H4A119.0 (13)C11—C12—H12A125.2 (11)
C4—C5—C6120.18 (17)N1—C12—H12A114.9 (11)
C4—C5—H5A119.9 (11)C12—C11—C10118.99 (16)
C6—C5—H5A119.9 (11)C12—C11—H11A122.1 (11)
O1—C7—O2123.33 (14)C10—C11—H11A118.9 (11)
O1—C7—C6118.52 (14)C9—C10—C11121.30 (16)
O2—C7—C6118.15 (13)C9—C10—H10A119.5 (10)
C10—C9—N3122.21 (15)C11—C10—H10A119.2 (10)
C10—C9—C8118.22 (14)
C5—C6—C1—C20.5 (2)C10—C9—C8—N2−179.52 (15)
C7—C6—C1—C2−179.77 (15)N3—C9—C8—N21.9 (2)
C6—C1—C2—C3−0.3 (3)C10—C9—C8—N11.4 (2)
C1—C2—C3—C4−0.1 (3)N3—C9—C8—N1−177.16 (13)
C2—C3—C4—C50.5 (3)N2—C8—N1—C12−179.52 (14)
C3—C4—C5—C6−0.3 (3)C9—C8—N1—C12−0.4 (2)
C1—C6—C5—C4−0.1 (3)C8—N1—C12—C11−0.4 (2)
C7—C6—C5—C4−179.90 (16)N1—C12—C11—C100.2 (2)
C1—C6—C7—O1−10.6 (2)N3—C9—C10—C11176.89 (15)
C5—C6—C7—O1169.17 (15)C8—C9—C10—C11−1.7 (2)
C1—C6—C7—O2169.17 (14)C12—C11—C10—C90.8 (3)
C5—C6—C7—O2−11.1 (2)
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O20.96 (2)1.77 (2)2.7218 (18)176 (2)
N2—H1N2···O10.90 (2)1.94 (2)2.8377 (18)173 (2)
N2—H2N2···O2i0.88 (2)2.01 (2)2.8873 (17)170 (2)
N3—H1N3···O2i0.91 (2)2.02 (2)2.9206 (19)173 (2)
N3—H2N3···O1ii0.95 (2)2.00 (2)2.9382 (19)170 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1N1⋯O20.96 (2)1.77 (2)2.7218 (18)176 (2)
N2—H1N2⋯O10.90 (2)1.94 (2)2.8377 (18)173 (2)
N2—H2N2⋯O2i0.88 (2)2.01 (2)2.8873 (17)170 (2)
N3—H1N3⋯O2i0.91 (2)2.02 (2)2.9206 (19)173 (2)
N3—H2N3⋯O1ii0.95 (2)2.00 (2)2.9382 (19)170 (2)

Symmetry codes: (i) ; (ii) .

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2.  2,3-Diamino-pyridinium benzoate benzoic acid solvate.

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Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-01-30

3.  2-Amino-3-ammonio-pyridinium dichloride.

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4.  2,3-Diamino-pyridinium 3-amino-benzoate.

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Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-07-01

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