Literature DB >> 22259470

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

Madhukar Hemamalini1, Jia Hao Goh, Hoong-Kun Fun.   

Abstract

In the title mol-ecular salt-adduct, C(5)H(8)N(3) (+)·C(6)H(7)O(2) (-)·C(6)H(8)O(2), the 2,3-diamino-pyridinium cation is essentially planar, with a maximum deviation of 0.013 (2) Å, and is protanated at its pyridine N atom. The sorbate anion and sorbic acid mol-ecules exist in extended conformations. In the crystal, 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(1) (2)(6) ring motif. The carboxyl groups of the sorbic acid mol-ecules and the carboxyl-ate groups of the sorbate anions are connected via O-H⋯O hydrogen bonds. Furthermore, the ion pairs and neutral mol-ecules are connected via inter-molecular N-H⋯O hydrogen bonds, forming sheets lying parallel to (100).

Entities:  

Year:  2011        PMID: 22259470      PMCID: PMC3254524          DOI: 10.1107/S1600536811053025

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


Related literature

For a different crystal structure arising from the same synthesis conditions, see: Hemamalini & Fun (2010 ▶). For background to amino­pyridines, see: Peng et al. (2001 ▶); Leung et al. (2002 ▶); Banerjee & Murugavel (2004 ▶); Lautie & Belabbes (1996 ▶). 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

C5H8N3C6H7O2 −·C6H8O2 M = 333.38 Monoclinic, a = 16.1636 (17) Å b = 9.6538 (10) Å c = 12.6887 (13) Å β = 112.844 (2)° V = 1824.6 (3) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 100 K 0.47 × 0.25 × 0.06 mm

Data collection

Bruker APEXII DUO CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.960, T max = 0.994 27805 measured reflections 5345 independent reflections 2898 reflections with I > 2σ(I) R int = 0.045

Refinement

R[F 2 > 2σ(F 2)] = 0.047 wR(F 2) = 0.152 S = 1.02 5345 reflections 239 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.30 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: SHELXTLand PLATON (Spek, 2009 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811053025/hb6558sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811053025/hb6558Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811053025/hb6558Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H8N3+·C6H7O2·C6H8O2F(000) = 712
Mr = 333.38Dx = 1.214 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4699 reflections
a = 16.1636 (17) Åθ = 2.5–23.6°
b = 9.6538 (10) ŵ = 0.09 mm1
c = 12.6887 (13) ÅT = 100 K
β = 112.844 (2)°Plate, brown
V = 1824.6 (3) Å30.47 × 0.25 × 0.06 mm
Z = 4
Bruker APEXII DUO CCD diffractometer5345 independent reflections
Radiation source: fine-focus sealed tube2898 reflections with I > 2σ(I)
graphiteRint = 0.045
φ and ω scansθmax = 30.1°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −22→22
Tmin = 0.960, Tmax = 0.994k = −13→13
27805 measured reflectionsl = −17→17
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.152H atoms treated by a mixture of independent and constrained refinement
S = 1.02w = 1/[σ2(Fo2) + (0.0631P)2 + 0.2243P] where P = (Fo2 + 2Fc2)/3
5345 reflections(Δ/σ)max < 0.001
239 parametersΔρmax = 0.30 e Å3
0 restraintsΔρmin = −0.22 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*/Ueq
N10.52439 (11)0.20084 (17)0.03419 (12)0.0703 (4)
N20.45891 (11)0.1854 (2)0.16546 (18)0.0778 (5)
N30.59685 (10)0.00896 (17)0.29774 (14)0.0713 (4)
C10.52362 (10)0.14816 (17)0.13081 (13)0.0563 (4)
C20.59314 (9)0.05457 (16)0.19419 (13)0.0522 (4)
C30.65504 (10)0.02052 (18)0.14930 (15)0.0642 (4)
H3A0.7001−0.04270.18780.077*
C40.65219 (12)0.0785 (2)0.04688 (16)0.0771 (5)
H4A0.69500.05480.01790.093*
C50.58688 (14)0.1688 (2)−0.00887 (16)0.0808 (5)
H5A0.58440.2092−0.07660.097*
O1B0.20615 (8)0.22997 (14)0.43760 (10)0.0701 (3)
O2B0.26440 (7)0.21636 (13)0.62722 (10)0.0698 (3)
C6B0.20207 (10)0.24501 (15)0.53806 (14)0.0541 (4)
C7B0.11588 (10)0.29993 (16)0.53419 (14)0.0560 (4)
H7BA0.07030.31650.46310.067*
C8B0.10027 (10)0.32670 (15)0.62678 (13)0.0536 (4)
H8BA0.14600.30660.69690.064*
C9B0.01845 (10)0.38450 (16)0.62879 (14)0.0569 (4)
H9BA−0.02770.40380.55880.068*
C10B0.00417 (13)0.41200 (19)0.72185 (16)0.0688 (5)
H10A0.05050.39250.79160.083*
C11B−0.07969 (15)0.4715 (3)0.7250 (2)0.0929 (7)
H11A−0.10590.40660.76040.139*
H11B−0.12130.49040.64850.139*
H11C−0.06600.55600.76830.139*
O1A0.35766 (7)0.14675 (14)0.44960 (11)0.0747 (4)
H1A0.30580.14180.44520.112*
O2A0.43810 (7)0.06465 (17)0.35977 (11)0.0830 (4)
C6A0.36773 (10)0.06657 (18)0.37630 (13)0.0588 (4)
C7A0.29051 (10)−0.02288 (17)0.31033 (13)0.0571 (4)
H7AA0.2396−0.01740.32730.068*
C8A0.28871 (10)−0.10933 (17)0.22971 (13)0.0571 (4)
H8AA0.3407−0.11710.21530.069*
C9A0.21322 (11)−0.19332 (17)0.16161 (14)0.0592 (4)
H9AA0.1603−0.18200.17330.071*
C10A0.21248 (13)−0.28488 (19)0.08416 (16)0.0716 (5)
H10B0.2656−0.29470.07260.086*
C11A0.13681 (15)−0.3735 (2)0.01381 (18)0.0891 (6)
H11G0.1245−0.3584−0.06570.134*
H11D0.0846−0.35070.02880.134*
H11E0.1521−0.46900.03250.134*
H1N10.4814 (17)0.260 (3)−0.006 (2)0.112 (8)*
H1N20.4194 (16)0.234 (2)0.1193 (19)0.093 (7)*
H2N20.4547 (15)0.148 (3)0.225 (2)0.098 (9)*
H1N30.5524 (13)0.0094 (18)0.3168 (15)0.066 (5)*
H2N30.6417 (15)−0.055 (3)0.3295 (19)0.104 (7)*
U11U22U33U12U13U23
N10.0674 (9)0.0770 (10)0.0511 (8)0.0190 (8)0.0062 (7)0.0022 (7)
N20.0622 (9)0.0905 (12)0.0739 (11)0.0316 (9)0.0190 (8)−0.0020 (10)
N30.0521 (8)0.0816 (11)0.0848 (11)0.0154 (8)0.0314 (8)0.0260 (9)
C10.0475 (8)0.0591 (9)0.0528 (9)0.0076 (7)0.0093 (6)−0.0078 (7)
C20.0435 (7)0.0516 (8)0.0558 (9)0.0029 (6)0.0132 (6)0.0003 (7)
C30.0476 (8)0.0699 (10)0.0708 (11)0.0105 (7)0.0181 (7)−0.0003 (9)
C40.0663 (11)0.1024 (15)0.0656 (11)0.0092 (10)0.0288 (9)−0.0031 (11)
C50.0818 (13)0.1025 (15)0.0527 (10)0.0082 (11)0.0203 (9)0.0028 (10)
O1B0.0584 (7)0.0927 (9)0.0518 (6)0.0105 (6)0.0133 (5)−0.0043 (6)
O2B0.0546 (6)0.0833 (8)0.0586 (7)0.0206 (6)0.0077 (5)0.0004 (6)
C6B0.0472 (8)0.0474 (8)0.0572 (9)0.0013 (6)0.0087 (7)−0.0020 (7)
C7B0.0465 (8)0.0593 (9)0.0530 (9)0.0042 (7)0.0091 (6)0.0043 (7)
C8B0.0484 (8)0.0488 (8)0.0542 (9)0.0001 (6)0.0097 (6)0.0031 (7)
C9B0.0530 (8)0.0559 (9)0.0571 (9)0.0014 (7)0.0163 (7)0.0059 (7)
C10B0.0731 (11)0.0684 (11)0.0661 (11)0.0056 (9)0.0283 (9)0.0067 (9)
C11B0.0984 (15)0.0950 (15)0.1081 (17)0.0154 (12)0.0648 (13)0.0127 (13)
O1A0.0507 (6)0.0923 (9)0.0765 (8)−0.0053 (6)0.0195 (6)−0.0293 (7)
O2A0.0473 (6)0.1230 (11)0.0829 (9)−0.0019 (7)0.0299 (6)−0.0065 (8)
C6A0.0473 (8)0.0721 (10)0.0563 (9)0.0017 (7)0.0194 (7)−0.0026 (8)
C7A0.0488 (8)0.0681 (10)0.0578 (9)0.0007 (7)0.0245 (7)−0.0049 (8)
C8A0.0536 (8)0.0649 (9)0.0525 (8)0.0105 (7)0.0201 (7)0.0031 (7)
C9A0.0641 (10)0.0571 (9)0.0553 (9)0.0064 (7)0.0218 (7)−0.0006 (7)
C10A0.0771 (12)0.0684 (11)0.0646 (10)0.0135 (9)0.0222 (9)−0.0041 (9)
C11A0.1050 (16)0.0634 (11)0.0814 (14)0.0037 (11)0.0172 (12)−0.0159 (10)
N1—C11.332 (2)C9B—C10B1.315 (2)
N1—C51.358 (2)C9B—H9BA0.9300
N1—H1N10.89 (3)C10B—C11B1.487 (3)
N2—C11.332 (2)C10B—H10A0.9300
N2—H1N20.83 (2)C11B—H11A0.9600
N2—H2N20.86 (2)C11B—H11B0.9600
N3—C21.365 (2)C11B—H11C0.9600
N3—H1N30.843 (18)O1A—C6A1.2682 (19)
N3—H2N30.92 (2)O1A—H1A0.8200
C1—C21.423 (2)O2A—C6A1.2341 (18)
C2—C31.370 (2)C6A—C7A1.481 (2)
C3—C41.399 (3)C7A—C8A1.312 (2)
C3—H3A0.9300C7A—H7AA0.9300
C4—C51.339 (3)C8A—C9A1.440 (2)
C4—H4A0.9300C8A—H8AA0.9300
C5—H5A0.9300C9A—C10A1.318 (2)
O1B—C6B1.310 (2)C9A—H9AA0.9300
O2B—C6B1.2192 (17)C10A—C11A1.475 (3)
C6B—C7B1.474 (2)C10A—H10B0.9300
C7B—C8B1.319 (2)C11A—H11G0.9600
C7B—H7BA0.9300C11A—H11D0.9600
C8B—C9B1.445 (2)C11A—H11E0.9600
C8B—H8BA0.9300
C1—N1—C5123.90 (16)C10B—C9B—H9BA117.5
C1—N1—H1N1119.1 (16)C8B—C9B—H9BA117.5
C5—N1—H1N1117.0 (16)C9B—C10B—C11B125.59 (18)
C1—N2—H1N2114.2 (15)C9B—C10B—H10A117.2
C1—N2—H2N2120.9 (16)C11B—C10B—H10A117.2
H1N2—N2—H2N2124 (2)C10B—C11B—H11A109.5
C2—N3—H1N3123.5 (12)C10B—C11B—H11B109.5
C2—N3—H2N3111.8 (14)H11A—C11B—H11B109.5
H1N3—N3—H2N3119.6 (19)C10B—C11B—H11C109.5
N2—C1—N1119.33 (16)H11A—C11B—H11C109.5
N2—C1—C2122.29 (17)H11B—C11B—H11C109.5
N1—C1—C2118.38 (15)C6A—O1A—H1A109.5
N3—C2—C3123.83 (15)O2A—C6A—O1A121.53 (16)
N3—C2—C1118.61 (14)O2A—C6A—C7A121.69 (15)
C3—C2—C1117.49 (15)O1A—C6A—C7A116.77 (13)
C2—C3—C4121.61 (16)C8A—C7A—C6A124.78 (14)
C2—C3—H3A119.2C8A—C7A—H7AA117.6
C4—C3—H3A119.2C6A—C7A—H7AA117.6
C5—C4—C3119.07 (17)C7A—C8A—C9A125.68 (15)
C5—C4—H4A120.5C7A—C8A—H8AA117.2
C3—C4—H4A120.5C9A—C8A—H8AA117.2
C4—C5—N1119.52 (19)C10A—C9A—C8A125.81 (17)
C4—C5—H5A120.2C10A—C9A—H9AA117.1
N1—C5—H5A120.2C8A—C9A—H9AA117.1
O2B—C6B—O1B122.84 (14)C9A—C10A—C11A127.25 (19)
O2B—C6B—C7B122.85 (15)C9A—C10A—H10B116.4
O1B—C6B—C7B114.30 (13)C11A—C10A—H10B116.4
C8B—C7B—C6B123.09 (14)C10A—C11A—H11G109.5
C8B—C7B—H7BA118.5C10A—C11A—H11D109.5
C6B—C7B—H7BA118.5H11G—C11A—H11D109.5
C7B—C8B—C9B125.75 (14)C10A—C11A—H11E109.5
C7B—C8B—H8BA117.1H11G—C11A—H11E109.5
C9B—C8B—H8BA117.1H11D—C11A—H11E109.5
C10B—C9B—C8B125.09 (16)
C5—N1—C1—N2−179.49 (19)O2B—C6B—C7B—C8B2.3 (2)
C5—N1—C1—C21.2 (3)O1B—C6B—C7B—C8B−177.53 (15)
N2—C1—C2—N3−4.5 (3)C6B—C7B—C8B—C9B177.96 (14)
N1—C1—C2—N3174.80 (15)C7B—C8B—C9B—C10B−179.26 (17)
N2—C1—C2—C3178.37 (17)C8B—C9B—C10B—C11B179.96 (18)
N1—C1—C2—C3−2.3 (2)O2A—C6A—C7A—C8A−0.6 (3)
N3—C2—C3—C4−174.93 (17)O1A—C6A—C7A—C8A178.42 (16)
C1—C2—C3—C42.0 (2)C6A—C7A—C8A—C9A−177.50 (15)
C2—C3—C4—C5−0.5 (3)C7A—C8A—C9A—C10A−176.71 (18)
C3—C4—C5—N1−0.8 (3)C8A—C9A—C10A—C11A179.34 (18)
C1—N1—C5—C40.4 (3)
D—H···AD—HH···AD···AD—H···A
O1A—H1A···O1B0.821.792.5252 (19)148
N1—H1N1···O1Ai0.89 (3)2.06 (3)2.887 (2)153 (3)
N1—H1N1···O2Ai0.89 (3)2.31 (3)3.094 (2)147 (2)
N2—H1N2···O1Ai0.83 (2)2.30 (2)3.054 (2)152 (2)
N2—H1N2···O2Bi0.83 (2)2.59 (3)3.136 (2)125 (2)
N2—H2N2···O2A0.86 (2)2.00 (3)2.863 (2)177 (2)
N3—H1N3···O2A0.84 (2)2.19 (2)3.010 (2)166.1 (16)
N3—H2N3···O2Bii0.92 (3)2.09 (3)3.002 (2)170 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O1A—H1A⋯O1B0.821.792.5252 (19)148
N1—H1N1⋯O1Ai0.89 (3)2.06 (3)2.887 (2)153 (3)
N1—H1N1⋯O2Ai0.89 (3)2.31 (3)3.094 (2)147 (2)
N2—H1N2⋯O1Ai0.83 (2)2.30 (2)3.054 (2)152 (2)
N2—H1N2⋯O2Bi0.83 (2)2.59 (3)3.136 (2)125 (2)
N2—H2N2⋯O2A0.86 (2)2.00 (3)2.863 (2)177 (2)
N3—H1N3⋯O2A0.84 (2)2.19 (2)3.010 (2)166.1 (16)
N3—H2N3⋯O2Bii0.92 (3)2.09 (3)3.002 (2)170 (2)

Symmetry codes: (i) ; (ii) .

  4 in total

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Authors:  Man-kit Leung; Ashis B Mandal; Chih-Chieh Wang; Gene-Hsiang Lee; Shie-Ming Peng; Hsing-Ling Cheng; Guor-Rong Her; Ito Chao; Hsiu-Feng Lu; Ying-Chieh Sun; Mei-Ying Shiao; Pi-Tai Chou
Journal:  J Am Chem Soc       Date:  2002-04-24       Impact factor: 15.419

2.  A short history of SHELX.

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

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

Authors:  Madhukar Hemamalini; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-08-21

4.  Structure validation in chemical crystallography.

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