Literature DB >> 21588709

2,3-Diamino-pyridinium (2E,4E)-hexa-2,4-dienoate.

Madhukar Hemamalini1, Hoong-Kun Fun.   

Abstract

In the title salt, C(5)H(8)N(3) (+)·C(6)H(7)O(2) (-), the pyridine N atom of the 2,3-diamino-pyridine mol-ecule is protonated. The 2,3-diamino-pyridinium cation is essentially planar, with a maximum deviation of 0.068 (2) Å for one of the amino N atoms. The sorbate anion adopts an extended conformation. In the crystal structure, the protonated N atom and one of the two amino-group H atoms are hydrogen bonded to the sorbate anion through a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. The ion pairs are further connected via inter-molecular N-H⋯O and C-H⋯O hydrogen bonds, forming two-dimensional networks parallel to (100).

Entities:  

Year:  2010        PMID: 21588709      PMCID: PMC3007997          DOI: 10.1107/S1600536810032617

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


Related literature

For details of non-covalent inter­actions, see: Desiraju (1995 ▶); Moulton & Zaworotko (2001 ▶); Biradha & Fujita (2002 ▶). For applications of sorbic acid, see: Martindale (1996 ▶); Richards (1972 ▶). For related structures, see: Cox (1994 ▶); Thanigaimani et al. (2007 ▶); Raj et al. (2003 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶). For standard bond-length data, see: Allen et al. (1987 ▶).

Experimental

Crystal data

C5H8N3C6H7O2 M = 221.26 Monoclinic, a = 9.0440 (3) Å b = 10.6964 (3) Å c = 12.4632 (4) Å β = 94.947 (2)° V = 1201.18 (6) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 296 K 0.15 × 0.15 × 0.09 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.987, T max = 0.993 8260 measured reflections 2736 independent reflections 1794 reflections with I > 2σ(I) R int = 0.053

Refinement

R[F 2 > 2σ(F 2)] = 0.049 wR(F 2) = 0.111 S = 1.02 2736 reflections 205 parameters All H-atom parameters refined Δρmax = 0.22 e Å−3 Δρmin = −0.22 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/S1600536810032617/lh5118sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536810032617/lh5118Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H8N3+·C6H7O2F(000) = 472
Mr = 221.26Dx = 1.224 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1444 reflections
a = 9.0440 (3) Åθ = 3.3–28.9°
b = 10.6964 (3) ŵ = 0.09 mm1
c = 12.4632 (4) ÅT = 296 K
β = 94.947 (2)°Block, red
V = 1201.18 (6) Å30.15 × 0.15 × 0.09 mm
Z = 4
Bruker SMART APEXII CCD area-detector diffractometer2736 independent reflections
Radiation source: fine-focus sealed tube1794 reflections with I > 2σ(I)
graphiteRint = 0.053
φ and ω scansθmax = 27.5°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −11→8
Tmin = 0.987, Tmax = 0.993k = −13→11
8260 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)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.111All H-atom parameters refined
S = 1.02w = 1/[σ2(Fo2) + (0.0417P)2 + 0.1735P] where P = (Fo2 + 2Fc2)/3
2736 reflections(Δ/σ)max < 0.001
205 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = −0.22 e Å3
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*/Ueq
O1−0.19667 (13)0.14636 (12)0.53361 (8)0.0233 (3)
O2−0.04642 (13)0.18916 (12)0.40526 (8)0.0241 (3)
C6−0.14500 (18)0.12200 (17)0.44625 (11)0.0180 (4)
H7−0.148 (2)−0.0069 (18)0.3182 (13)0.026 (5)*
H8−0.364 (2)−0.0391 (18)0.4703 (14)0.030 (5)*
H9−0.317 (2)−0.1811 (18)0.2736 (14)0.028 (5)*
H10−0.545 (2)−0.2085 (19)0.4233 (15)0.037 (6)*
H11A−0.672 (3)−0.307 (2)0.2669 (16)0.050 (6)*
H11B−0.556 (2)−0.407 (2)0.3260 (14)0.031 (5)*
H11C−0.507 (2)−0.3389 (19)0.2230 (15)0.034 (5)*
C7−0.1975 (2)0.01064 (18)0.38280 (12)0.0224 (4)
C8−0.3120 (2)−0.06038 (18)0.40571 (12)0.0209 (4)
C9−0.3730 (2)−0.16160 (17)0.33880 (13)0.0219 (4)
C10−0.4924 (2)−0.22749 (18)0.35940 (14)0.0252 (4)
C11−0.5606 (2)−0.3280 (2)0.28818 (17)0.0309 (5)
H2N30.224 (2)0.516 (2)0.8425 (15)0.035 (6)*
N10.09874 (16)0.36086 (15)0.52745 (10)0.0212 (4)
N20.00087 (17)0.28443 (16)0.67865 (12)0.0236 (4)
N30.1886 (2)0.44680 (19)0.80698 (11)0.0286 (4)
C10.1867 (2)0.43933 (19)0.47441 (14)0.0278 (5)
C20.2698 (2)0.5265 (2)0.52935 (15)0.0324 (5)
C30.2682 (2)0.53273 (19)0.64186 (14)0.0276 (5)
C40.18421 (19)0.45140 (18)0.69625 (12)0.0222 (4)
C50.09207 (18)0.36429 (17)0.63493 (12)0.0193 (4)
H10.178 (2)0.4288 (18)0.3983 (14)0.027 (5)*
H20.324 (2)0.586 (2)0.4933 (15)0.038 (6)*
H30.326 (2)0.599 (2)0.6825 (14)0.032 (5)*
H1N10.039 (2)0.297 (2)0.4839 (15)0.037 (6)*
H1N2−0.021 (2)0.291 (2)0.7442 (17)0.038 (6)*
H2N2−0.065 (2)0.236 (2)0.6330 (16)0.036 (6)*
H1N30.113 (3)0.407 (2)0.8330 (16)0.049 (7)*
U11U22U33U12U13U23
O10.0270 (7)0.0241 (8)0.0191 (5)−0.0026 (6)0.0040 (5)−0.0010 (5)
O20.0274 (7)0.0258 (8)0.0193 (5)−0.0058 (6)0.0023 (5)0.0002 (5)
C60.0193 (9)0.0172 (11)0.0170 (7)0.0011 (8)−0.0020 (6)0.0033 (7)
C70.0238 (10)0.0241 (12)0.0190 (7)0.0022 (9)0.0005 (7)−0.0010 (7)
C80.0206 (9)0.0205 (12)0.0211 (7)0.0050 (8)−0.0006 (7)0.0010 (7)
C90.0237 (10)0.0191 (12)0.0225 (8)0.0016 (8)0.0002 (7)−0.0009 (7)
C100.0243 (10)0.0218 (12)0.0295 (9)0.0013 (9)0.0023 (7)0.0001 (8)
C110.0272 (11)0.0276 (14)0.0373 (10)−0.0041 (10)−0.0007 (9)−0.0009 (10)
N10.0237 (8)0.0201 (9)0.0197 (6)−0.0022 (7)0.0010 (6)−0.0009 (6)
N20.0252 (9)0.0272 (11)0.0187 (7)−0.0052 (8)0.0034 (6)−0.0046 (7)
N30.0309 (10)0.0300 (11)0.0246 (7)−0.0088 (8)0.0012 (7)−0.0094 (7)
C10.0320 (11)0.0280 (13)0.0235 (8)−0.0025 (9)0.0033 (8)0.0042 (8)
C20.0346 (12)0.0280 (14)0.0351 (9)−0.0075 (10)0.0053 (9)0.0068 (9)
C30.0293 (11)0.0183 (12)0.0346 (9)−0.0039 (9)−0.0001 (8)−0.0032 (8)
C40.0207 (9)0.0206 (11)0.0249 (8)0.0029 (8)0.0003 (7)−0.0029 (8)
C50.0185 (9)0.0167 (11)0.0223 (7)0.0030 (8)0.0006 (6)−0.0012 (7)
O1—C61.2488 (18)N1—C11.366 (2)
O2—C61.285 (2)N1—H1N11.00 (2)
C6—C71.485 (2)N2—C51.336 (2)
C7—C81.335 (2)N2—H1N20.86 (2)
C7—H70.974 (17)N2—H2N20.95 (2)
C8—C91.446 (2)N3—C41.378 (2)
C8—H80.993 (18)N3—H2N30.91 (2)
C9—C101.333 (3)N3—H1N30.89 (3)
C9—H91.017 (18)C1—C21.347 (3)
C10—C111.493 (3)C1—H10.952 (16)
C10—H100.982 (19)C2—C31.405 (2)
C11—H11A1.04 (2)C2—H20.94 (2)
C11—H11B0.97 (2)C3—C41.372 (3)
C11—H11C0.99 (2)C3—H30.99 (2)
N1—C51.3466 (19)C4—C51.427 (2)
O1—C6—O2123.69 (16)C1—N1—H1N1117.8 (11)
O1—C6—C7120.34 (15)C5—N2—H1N2122.4 (14)
O2—C6—C7115.97 (14)C5—N2—H2N2119.2 (12)
C8—C7—C6124.12 (15)H1N2—N2—H2N2115.5 (18)
C8—C7—H7119.4 (11)C4—N3—H2N3116.1 (12)
C6—C7—H7116.4 (11)C4—N3—H1N3115.1 (14)
C7—C8—C9124.52 (16)H2N3—N3—H1N3117.3 (19)
C7—C8—H8118.2 (11)C2—C1—N1120.15 (16)
C9—C8—H8117.1 (11)C2—C1—H1125.5 (12)
C10—C9—C8124.02 (16)N1—C1—H1114.3 (12)
C10—C9—H9121.0 (11)C1—C2—C3119.12 (19)
C8—C9—H9114.9 (11)C1—C2—H2121.0 (12)
C9—C10—C11124.47 (17)C3—C2—H2119.8 (12)
C9—C10—H10120.1 (12)C4—C3—C2121.12 (19)
C11—C10—H10115.3 (12)C4—C3—H3119.4 (11)
C10—C11—H11A109.4 (13)C2—C3—H3119.5 (11)
C10—C11—H11B110.0 (11)C3—C4—N3123.23 (17)
H11A—C11—H11B108.2 (17)C3—C4—C5118.16 (15)
C10—C11—H11C111.7 (11)N3—C4—C5118.57 (17)
H11A—C11—H11C110.2 (16)N2—C5—N1118.07 (16)
H11B—C11—H11C107.3 (16)N2—C5—C4123.47 (15)
C5—N1—C1122.86 (16)N1—C5—C4118.45 (16)
C5—N1—H1N1119.3 (11)
O1—C6—C7—C88.5 (3)C2—C3—C4—N3174.29 (19)
O2—C6—C7—C8−171.14 (16)C2—C3—C4—C5−3.3 (3)
C6—C7—C8—C9173.77 (16)C1—N1—C5—N2179.13 (17)
C7—C8—C9—C10−176.15 (18)C1—N1—C5—C4−1.8 (3)
C8—C9—C10—C11176.92 (18)C3—C4—C5—N2−177.03 (18)
C5—N1—C1—C2−1.2 (3)N3—C4—C5—N25.3 (3)
N1—C1—C2—C32.0 (3)C3—C4—C5—N14.0 (3)
C1—C2—C3—C40.3 (3)N3—C4—C5—N1−173.69 (16)
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O21.00 (2)1.66 (2)2.6591 (19)174.7 (18)
N2—H1N2···O2i0.86 (2)2.05 (2)2.9065 (18)173.1 (17)
N2—H2N2···O10.94 (2)1.90 (2)2.8432 (19)176.2 (18)
N3—H1N3···O2i0.89 (2)2.04 (2)2.930 (2)174 (2)
N3—H2N3···O1ii0.91 (2)2.11 (2)2.913 (2)146.9 (16)
C10—H10···O1iii0.983 (19)2.531 (18)3.330 (2)138.2 (14)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1N1⋯O21.00 (2)1.66 (2)2.6591 (19)174.7 (18)
N2—H1N2⋯O20.86 (2)2.05 (2)2.9065 (18)173.1 (17)
N2—H2N2⋯O10.94 (2)1.90 (2)2.8432 (19)176.2 (18)
N3—H1N3⋯O20.89 (2)2.04 (2)2.930 (2)174 (2)
N3—H2N3⋯O1i0.91 (2)2.11 (2)2.913 (2)146.9 (16)
C10—H10⋯O1ii0.983 (19)2.531 (18)3.330 (2)138.2 (14)

Symmetry codes: (i) ; (ii) .

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1.  2,3-Diamino-pyridinium sorbate-sorbic acid (1/1).

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