Literature DB >> 21583446

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

Kasthuri Balasubramani1, Hoong-Kun Fun.   

Abstract

In the title salt, C(5)n class="Species">H(8)N(3) (+)·C(7)H(6)NO(2) (-), the pyridine N atom of the 2,3-diamino-pyridine mol-ecule is protonated. The proton-ated N atom and one of the two N atoms of the 2-amino groups are hydrogen bonded to the 3-amino-benzoate anion through a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. The carboxyl-ate mean plane of the 3-amino-benzoate anion is twisted by 8.81 (7)° from the attached ring. The crystal structure is further stabilized by π-π inter-actions [centroid-centroid distance 3.6827 (7) Å].

Entities:  

Year:  2009        PMID: 21583446      PMCID: PMC2977358          DOI: 10.1107/S1600536809024362

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


Related literature

For substituted pyridines, see: Pozharski et al. (1997 ▶); Katritzky et al. (1996 ▶). For n class="Chemical">hydrogen bonding in pyridine and its substituted derivatives, see: Jeffrey & Saenger (1991 ▶); Jeffrey (1997 ▶); Scheiner (1997 ▶). For related structures, see: Fun & Balasubramani (2009 ▶); Balasubramani & Fun (2009a ▶,b ▶). For bond-length data, see: Allen et al. (1987 ▶). 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

C5H8N3n class="Chemical">C7H6NO2 − M = 246.27 Monoclinic, a = 9.9119 (2) Å b = 10.1751 (2) Å c = 12.4060 (2) Å β = 106.811 (1)° V = 1197.73 (4) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 100 K 0.46 × 0.14 × 0.06 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2005 ▶) T min = 0.957, T max = 0.994 19514 measured reflections 4434 independent reflections 2965 reflections with I > 2σ(I) R int = 0.046

Refinement

R[F 2 > 2σ(F 2)] = 0.050 wR(F 2) = 0.142 S = 1.06 4434 reflections 219 parameters All H-atom parameters refined Δρmax = 0.33 e Å−3 Δρmin = −0.23 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/S1600536809024362/bt2977sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809024362/bt2977Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H8N3+·C7H6NO2F(000) = 520
Mr = 246.27Dx = 1.366 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3436 reflections
a = 9.9119 (2) Åθ = 2.9–32.6°
b = 10.1751 (2) ŵ = 0.10 mm1
c = 12.4060 (2) ÅT = 100 K
β = 106.811 (1)°Plate, brown
V = 1197.73 (4) Å30.46 × 0.14 × 0.06 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer4434 independent reflections
Radiation source: fine-focus sealed tube2965 reflections with I > 2σ(I)
graphiteRint = 0.046
φ and ω scansθmax = 32.8°, θmin = 2.2°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −14→15
Tmin = 0.957, Tmax = 0.994k = −12→15
19514 measured reflectionsl = −18→18
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.142All H-atom parameters refined
S = 1.06w = 1/[σ2(Fo2) + (0.0681P)2 + 0.0752P] where P = (Fo2 + 2Fc2)/3
4434 reflections(Δ/σ)max < 0.001
219 parametersΔρmax = 0.33 e Å3
0 restraintsΔρmin = −0.23 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 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
N10.45804 (11)0.32315 (11)0.46427 (8)0.0219 (2)
N20.56864 (12)0.28026 (12)0.32806 (9)0.0252 (2)
N30.36894 (13)0.43692 (12)0.17546 (9)0.0275 (2)
C80.46690 (12)0.34222 (12)0.35929 (10)0.0199 (2)
C90.36669 (13)0.42721 (12)0.28567 (10)0.0223 (2)
C100.26897 (14)0.48893 (14)0.32782 (11)0.0276 (3)
C110.26420 (14)0.46612 (14)0.43889 (12)0.0286 (3)
C120.35938 (13)0.38245 (13)0.50509 (11)0.0252 (3)
H100.1974 (16)0.5508 (16)0.2749 (13)0.032 (4)*
H110.1881 (16)0.5151 (16)0.4685 (13)0.033 (4)*
H120.3671 (16)0.3657 (15)0.5851 (13)0.028 (4)*
H1N10.5279 (18)0.2611 (17)0.5122 (14)0.040 (5)*
H1N20.6338 (18)0.2303 (17)0.3822 (15)0.040 (5)*
H2N20.5864 (19)0.2985 (18)0.2620 (16)0.045 (5)*
H1N30.453 (2)0.4228 (19)0.1593 (16)0.056 (6)*
H2N30.311 (2)0.504 (2)0.1305 (16)0.053 (5)*
C40.96875 (12)−0.19646 (13)0.66376 (10)0.0226 (2)
C50.89408 (12)−0.08847 (12)0.60585 (10)0.0206 (2)
H10.7131 (18)−0.0025 (17)0.7829 (14)0.042 (5)*
H20.8458 (18)−0.1824 (17)0.8828 (15)0.039 (4)*
H31.0060 (16)−0.3052 (16)0.8108 (13)0.032 (4)*
H50.9082 (15)−0.0651 (14)0.5321 (12)0.023 (4)*
C60.80059 (12)−0.01887 (12)0.64902 (9)0.0191 (2)
C70.72259 (12)0.09741 (12)0.58352 (9)0.0198 (2)
O10.75796 (9)0.13487 (9)0.49856 (7)0.0232 (2)
O20.62586 (10)0.15115 (9)0.61617 (7)0.0259 (2)
N41.05563 (14)−0.26916 (14)0.61717 (11)0.0347 (3)
C10.78080 (13)−0.05510 (13)0.75193 (10)0.0231 (2)
C20.85824 (14)−0.16013 (13)0.81132 (11)0.0261 (3)
C30.94998 (13)−0.23049 (13)0.76778 (11)0.0249 (3)
H1N41.097 (2)−0.224 (2)0.5680 (17)0.057 (6)*
H2N41.109 (2)−0.329 (2)0.6604 (17)0.053 (5)*
U11U22U33U12U13U23
N10.0232 (5)0.0234 (5)0.0198 (5)0.0005 (4)0.0075 (4)0.0013 (4)
N20.0283 (5)0.0289 (6)0.0206 (5)0.0065 (4)0.0105 (4)0.0062 (4)
N30.0298 (6)0.0314 (6)0.0196 (5)0.0039 (5)0.0045 (4)0.0048 (4)
C80.0208 (5)0.0193 (5)0.0196 (5)−0.0018 (4)0.0059 (4)0.0005 (4)
C90.0225 (5)0.0220 (6)0.0204 (5)−0.0007 (5)0.0031 (4)0.0010 (4)
C100.0238 (6)0.0285 (7)0.0283 (6)0.0038 (5)0.0041 (5)0.0003 (5)
C110.0252 (6)0.0307 (7)0.0310 (7)0.0016 (5)0.0097 (5)−0.0041 (5)
C120.0262 (6)0.0280 (7)0.0234 (6)−0.0009 (5)0.0104 (5)−0.0029 (5)
C40.0201 (5)0.0230 (6)0.0257 (6)−0.0015 (5)0.0083 (4)0.0014 (5)
C50.0209 (5)0.0223 (6)0.0187 (5)−0.0014 (4)0.0057 (4)0.0012 (4)
C60.0200 (5)0.0196 (5)0.0171 (5)−0.0019 (4)0.0043 (4)−0.0002 (4)
C70.0231 (5)0.0207 (6)0.0151 (5)−0.0020 (4)0.0046 (4)−0.0015 (4)
O10.0251 (4)0.0266 (5)0.0183 (4)0.0010 (4)0.0072 (3)0.0034 (3)
O20.0318 (5)0.0272 (5)0.0213 (4)0.0078 (4)0.0116 (4)0.0033 (3)
N40.0351 (6)0.0352 (7)0.0405 (7)0.0139 (5)0.0216 (5)0.0126 (6)
C10.0257 (6)0.0234 (6)0.0217 (6)0.0010 (5)0.0096 (5)0.0016 (5)
C20.0302 (6)0.0279 (7)0.0223 (6)0.0012 (5)0.0107 (5)0.0061 (5)
C30.0235 (6)0.0243 (6)0.0273 (6)0.0016 (5)0.0078 (5)0.0067 (5)
N1—C81.3445 (15)C4—N41.3822 (17)
N1—C121.3650 (16)C4—C31.3995 (17)
N1—H1N10.997 (18)C4—C51.4013 (17)
N2—C81.3382 (16)C5—C61.3907 (16)
N2—H1N20.936 (18)C5—H50.994 (14)
N2—H2N20.906 (19)C6—C11.3961 (16)
N3—C91.3775 (16)C6—C71.5147 (17)
N3—H1N30.92 (2)C7—O11.2621 (14)
N3—H2N30.96 (2)C7—O21.2677 (14)
C8—C91.4296 (16)N4—H1N40.95 (2)
C9—C101.3781 (18)N4—H2N40.88 (2)
C10—C111.4115 (19)C1—C21.3954 (18)
C10—H101.030 (16)C1—H11.017 (17)
C11—C121.3569 (19)C2—C31.3839 (18)
C11—H111.054 (16)C2—H20.957 (17)
C12—H120.988 (15)C3—H31.000 (16)
C8—N1—C12123.37 (11)N4—C4—C3121.21 (12)
C8—N1—H1N1116.1 (10)N4—C4—C5120.39 (11)
C12—N1—H1N1120.5 (10)C3—C4—C5118.38 (11)
C8—N2—H1N2118.0 (10)C6—C5—C4120.92 (11)
C8—N2—H2N2121.7 (12)C6—C5—H5121.3 (8)
H1N2—N2—H2N2119.1 (15)C4—C5—H5117.7 (8)
C9—N3—H1N3118.6 (12)C5—C6—C1120.21 (11)
C9—N3—H2N3116.7 (11)C5—C6—C7118.99 (10)
H1N3—N3—H2N3114.2 (16)C1—C6—C7120.79 (11)
N2—C8—N1118.57 (11)O1—C7—O2123.71 (11)
N2—C8—C9122.86 (11)O1—C7—C6117.51 (10)
N1—C8—C9118.57 (11)O2—C7—C6118.77 (10)
N3—C9—C10123.98 (12)C4—N4—H1N4116.5 (12)
N3—C9—C8118.02 (11)C4—N4—H2N4117.0 (12)
C10—C9—C8117.90 (11)H1N4—N4—H2N4115.6 (17)
C9—C10—C11121.41 (12)C2—C1—C6118.93 (12)
C9—C10—H10117.8 (8)C2—C1—H1121.7 (10)
C11—C10—H10120.8 (8)C6—C1—H1119.3 (10)
C12—C11—C10118.71 (12)C3—C2—C1120.88 (12)
C12—C11—H11121.8 (9)C3—C2—H2121.0 (10)
C10—C11—H11119.4 (9)C1—C2—H2118.1 (10)
C11—C12—N1120.00 (12)C2—C3—C4120.64 (12)
C11—C12—H12123.7 (9)C2—C3—H3120.7 (9)
N1—C12—H12116.1 (9)C4—C3—H3118.6 (9)
C12—N1—C8—N2179.31 (11)C4—C5—C6—C10.65 (18)
C12—N1—C8—C9−1.04 (17)C4—C5—C6—C7179.83 (11)
N2—C8—C9—N35.26 (18)C5—C6—C7—O1−7.75 (16)
N1—C8—C9—N3−174.37 (11)C1—C6—C7—O1171.43 (11)
N2—C8—C9—C10−178.13 (12)C5—C6—C7—O2171.97 (11)
N1—C8—C9—C102.23 (17)C1—C6—C7—O2−8.85 (17)
N3—C9—C10—C11174.31 (12)C5—C6—C1—C21.28 (18)
C8—C9—C10—C11−2.08 (19)C7—C6—C1—C2−177.89 (11)
C9—C10—C11—C120.7 (2)C6—C1—C2—C3−2.1 (2)
C10—C11—C12—N10.6 (2)C1—C2—C3—C41.0 (2)
C8—N1—C12—C11−0.41 (19)N4—C4—C3—C2−177.33 (13)
N4—C4—C5—C6176.53 (12)C5—C4—C3—C20.93 (19)
C3—C4—C5—C6−1.75 (18)
D—H···AD—HH···AD···AD—H···A
N2—H2N2···O2i0.91 (2)2.02 (2)2.9293 (14)177.1 (17)
N3—H1N3···O2i0.92 (2)2.08 (2)2.9854 (16)167.3 (18)
N3—H2N3···O1ii0.96 (2)2.04 (2)2.9544 (14)158.1 (16)
N4—H1N4···O1iii0.95 (2)2.06 (2)2.9794 (15)162.3 (18)
N1—H1N1···O20.99 (2)1.77 (2)2.7510 (13)167.1 (15)
N2—H1N2···O10.94 (2)1.87 (2)2.8086 (14)175.7 (16)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N2—H2N2⋯O2i0.91 (2)2.02 (2)2.9293 (14)177.1 (17)
N3—H1N3⋯O2i0.92 (2)2.08 (2)2.9854 (16)167.3 (18)
N3—H2N3⋯O1ii0.96 (2)2.04 (2)2.9544 (14)158.1 (16)
N4—H1N4⋯O1iii0.95 (2)2.06 (2)2.9794 (15)162.3 (18)
N1—H1N1⋯O20.99 (2)1.77 (2)2.7510 (13)167.1 (15)
N2—H1N2⋯O10.94 (2)1.87 (2)2.8086 (14)175.7 (16)

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

  5 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.  2,3-Diamino-pyridinium benzoate.

Authors:  Kasthuri Balasubramani; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-06-06

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

Authors:  Kasthuri Balasubramani; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-06-06

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

Authors:  Hoong-Kun Fun; Kasthuri Balasubramani
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-06-06

5.  Structure validation in chemical crystallography.

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

1.  2-Amino-5-bromo-pyridinium 3-amino-benzoate.

Authors:  Madhukar Hemamalini; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-02-20
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.