Literature DB >> 22347022

Bis(2,3-diamino-pyridinium) phthalate dihydrate.

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

Abstract

The complete anion of the title hydrated mol-ecular salt, 2C(5)H(8)N(3) (+)·C(8)H(4)O(4) (-)·2H(2)O, is generated by a crystallographic twofold axis. In the crystal, the cations, anions and water mol-ecules are connected by N-H⋯O, O-H⋯O and C-H⋯O hydrogen bonds, forming a three-dimensional network. The crystal structure also features C-H⋯π inter-actions.

Entities:  

Year:  2012        PMID: 22347022      PMCID: PMC3275077          DOI: 10.1107/S1600536811055838

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


Related literature

For background to hydrogen-bonding patterns of 2-amino­pyridine derivatives, see: Gellert & Hsu (1988 ▶); Banerjee & Murugavel (2004 ▶). For related structures, see: Hemamalini & Fun (2010a ▶,b ▶,c ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

2C5H8N3 +·C8H4O4 −·2H2O M = 420.43 Monoclinic, a = 15.795 (5) Å b = 13.083 (4) Å c = 11.012 (4) Å β = 115.194 (5)° V = 2059.2 (11) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 100 K 0.42 × 0.36 × 0.03 mm

Data collection

Bruker APEXII DUO CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.958, T max = 0.997 10343 measured reflections 2955 independent reflections 2148 reflections with I > 2σ(I) R int = 0.042

Refinement

R[F 2 > 2σ(F 2)] = 0.043 wR(F 2) = 0.125 S = 1.04 2955 reflections 184 parameters All H-atom parameters refined Δρmax = 0.33 e Å−3 Δρmin = −0.26 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 datablock(s) global, I. DOI: 10.1107/S1600536811055838/hb6574sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811055838/hb6574Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811055838/hb6574Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
2C5H8N3+·C8H4O4·2H2OF(000) = 888
Mr = 420.43Dx = 1.356 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 3390 reflections
a = 15.795 (5) Åθ = 2.8–29.8°
b = 13.083 (4) ŵ = 0.10 mm1
c = 11.012 (4) ÅT = 100 K
β = 115.194 (5)°Plate, brown
V = 2059.2 (11) Å30.42 × 0.36 × 0.03 mm
Z = 4
Bruker APEXII DUO CCD diffractometer2955 independent reflections
Radiation source: fine-focus sealed tube2148 reflections with I > 2σ(I)
graphiteRint = 0.042
φ and ω scansθmax = 29.9°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −22→22
Tmin = 0.958, Tmax = 0.997k = −18→18
10343 measured reflectionsl = −14→14
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.125All H-atom parameters refined
S = 1.03w = 1/[σ2(Fo2) + (0.0653P)2 + 0.7423P] where P = (Fo2 + 2Fc2)/3
2955 reflections(Δ/σ)max < 0.001
184 parametersΔρmax = 0.33 e Å3
0 restraintsΔρmin = −0.25 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
N10.23077 (8)0.94380 (9)1.03746 (11)0.0227 (3)
N20.30262 (8)0.94315 (10)0.89459 (13)0.0256 (3)
N30.17815 (10)0.78666 (11)0.74285 (14)0.0330 (3)
C10.23819 (9)0.90400 (10)0.93023 (13)0.0192 (3)
C20.17516 (9)0.82430 (9)0.85688 (13)0.0210 (3)
C30.11106 (9)0.79131 (11)0.90331 (14)0.0249 (3)
C40.10585 (11)0.83570 (13)1.01540 (15)0.0313 (3)
C50.16621 (11)0.91224 (13)1.08149 (15)0.0310 (3)
O10.43751 (6)0.07071 (7)0.10193 (9)0.0225 (2)
O20.32273 (6)0.12167 (7)0.15491 (9)0.0225 (2)
C60.45346 (10)0.41720 (10)0.20469 (14)0.0242 (3)
C70.40590 (9)0.32537 (10)0.16012 (13)0.0201 (3)
C80.45249 (8)0.23274 (9)0.20552 (12)0.0160 (2)
C90.40094 (8)0.13405 (9)0.15149 (12)0.0168 (2)
O1W0.45043 (8)0.10881 (8)0.86130 (12)0.0315 (3)
H10.3388 (12)0.3242 (12)0.0959 (17)0.028 (4)*
H20.0692 (11)0.7346 (13)0.8557 (17)0.026 (4)*
H30.4209 (12)0.4807 (14)0.1749 (17)0.032 (4)*
H40.1689 (13)0.9496 (15)1.160 (2)0.043 (5)*
H50.3138 (13)0.9165 (14)0.8275 (19)0.033 (5)*
H60.2697 (12)1.0029 (15)1.0806 (18)0.036 (5)*
H70.3468 (13)0.9879 (15)0.9506 (19)0.039 (5)*
H80.0557 (13)0.8149 (14)1.044 (2)0.042 (5)*
H90.1404 (14)0.7328 (17)0.712 (2)0.046 (5)*
H100.2265 (14)0.7967 (14)0.723 (2)0.040 (5)*
H110.4555 (16)0.1035 (17)0.950 (3)0.064 (7)*
H120.4828 (16)0.0542 (18)0.850 (2)0.062 (7)*
U11U22U33U12U13U23
N10.0235 (6)0.0244 (6)0.0181 (5)−0.0068 (5)0.0070 (4)−0.0020 (4)
N20.0237 (6)0.0281 (6)0.0260 (6)−0.0104 (5)0.0116 (5)−0.0096 (5)
N30.0323 (7)0.0332 (7)0.0364 (7)−0.0153 (6)0.0174 (6)−0.0188 (6)
C10.0186 (6)0.0182 (6)0.0175 (6)−0.0001 (4)0.0043 (5)0.0016 (4)
C20.0195 (6)0.0181 (6)0.0197 (6)−0.0001 (5)0.0028 (5)0.0004 (5)
C30.0232 (6)0.0223 (6)0.0224 (6)−0.0060 (5)0.0033 (5)0.0024 (5)
C40.0312 (7)0.0392 (8)0.0237 (7)−0.0138 (6)0.0119 (6)0.0001 (6)
C50.0348 (8)0.0393 (8)0.0223 (7)−0.0128 (6)0.0153 (6)−0.0043 (6)
O10.0229 (5)0.0220 (5)0.0222 (5)−0.0006 (4)0.0093 (4)−0.0059 (4)
O20.0205 (4)0.0227 (5)0.0253 (5)−0.0041 (4)0.0106 (4)−0.0029 (4)
C60.0252 (7)0.0173 (6)0.0297 (7)0.0038 (5)0.0113 (6)0.0033 (5)
C70.0191 (6)0.0200 (6)0.0196 (6)0.0017 (5)0.0068 (5)0.0022 (4)
C80.0180 (6)0.0171 (6)0.0140 (5)−0.0005 (4)0.0078 (4)−0.0002 (4)
C90.0178 (5)0.0173 (6)0.0124 (5)0.0007 (4)0.0036 (4)0.0006 (4)
O1W0.0361 (6)0.0276 (6)0.0363 (6)0.0102 (4)0.0208 (5)0.0120 (4)
N1—C11.3404 (17)C4—H81.01 (2)
N1—C51.3663 (18)C5—H40.98 (2)
N1—H60.98 (2)O1—C91.2596 (15)
N2—C11.3388 (17)O2—C91.2623 (15)
N2—H50.899 (19)C6—C6i1.382 (3)
N2—H70.92 (2)C6—C71.3910 (19)
N3—C21.3683 (19)C6—H30.959 (18)
N3—H90.89 (2)C7—C81.3954 (17)
N3—H100.89 (2)C7—H10.993 (17)
C1—C21.4304 (18)C8—C8i1.400 (2)
C2—C31.383 (2)C8—C91.5072 (17)
C3—C41.398 (2)O1W—H110.95 (3)
C3—H20.983 (17)O1W—H120.91 (2)
C4—C51.360 (2)
C1—N1—C5123.61 (12)C5—C4—H8119.7 (11)
C1—N1—H6117.6 (11)C3—C4—H8121.0 (11)
C5—N1—H6118.5 (10)C4—C5—N1119.44 (14)
C1—N2—H5122.2 (12)C4—C5—H4126.7 (11)
C1—N2—H7120.2 (11)N1—C5—H4113.8 (11)
H5—N2—H7116.0 (16)C6i—C6—C7120.25 (8)
C2—N3—H9111.0 (13)C6i—C6—H3119.9 (10)
C2—N3—H10122.9 (13)C7—C6—H3119.8 (10)
H9—N3—H10121.6 (18)C6—C7—C8120.03 (12)
N2—C1—N1118.16 (12)C6—C7—H1121.1 (10)
N2—C1—C2123.13 (12)C8—C7—H1118.9 (10)
N1—C1—C2118.67 (12)C7—C8—C8i119.70 (7)
N3—C2—C3122.93 (12)C7—C8—C9119.26 (11)
N3—C2—C1119.54 (12)C8i—C8—C9120.95 (6)
C3—C2—C1117.49 (12)O1—C9—O2124.30 (11)
C2—C3—C4121.61 (13)O1—C9—C8117.67 (11)
C2—C3—H2118.0 (10)O2—C9—C8117.99 (11)
C4—C3—H2120.4 (10)H11—O1W—H12105.6 (19)
C5—C4—C3119.14 (13)
C5—N1—C1—N2178.22 (13)C3—C4—C5—N1−0.3 (2)
C5—N1—C1—C20.2 (2)C1—N1—C5—C40.6 (2)
N2—C1—C2—N3−1.5 (2)C6i—C6—C7—C8−0.9 (2)
N1—C1—C2—N3176.36 (12)C6—C7—C8—C8i−0.9 (2)
N2—C1—C2—C3−179.27 (13)C6—C7—C8—C9−177.35 (12)
N1—C1—C2—C3−1.39 (18)C7—C8—C9—O1126.40 (13)
N3—C2—C3—C4−175.91 (14)C8i—C8—C9—O1−50.01 (19)
C1—C2—C3—C41.8 (2)C7—C8—C9—O2−51.38 (16)
C2—C3—C4—C5−0.9 (2)C8i—C8—C9—O2132.22 (15)
Cg1 and Cg2 are the centroids of the C6–C8/C6A–C8A and N1/C1–C5 rings, respectively.
D—H···AD—HH···AD···AD—H···A
N2—H5···O2ii0.90 (2)2.03 (2)2.9155 (19)169.0 (18)
N1—H6···O2iii0.98 (2)1.790 (19)2.7565 (18)170.3 (19)
N2—H7···O1iii0.92 (2)1.99 (2)2.8976 (19)168.1 (19)
N3—H9···O1Wiv0.89 (2)2.09 (2)2.978 (2)179 (3)
N3—H10···O2ii0.89 (2)2.23 (2)3.078 (2)158.8 (17)
O1W—H11···O1v0.95 (3)1.86 (3)2.7878 (18)165 (3)
O1W—H12···O1vi0.92 (2)1.99 (2)2.8641 (18)158.2 (19)
C3—H2···O1Wvii0.984 (17)2.516 (18)3.369 (2)145.0 (14)
C4—H8···Cg1iv1.01 (2)2.76 (2)3.629 (2)144.3 (15)
C6—H3···Cg2viii0.959 (18)2.568 (18)3.497 (2)163.4 (14)
Table 1

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the C6–C8/C6A–C8A and N1/C1–C5 rings, respectively.

D—H⋯AD—HH⋯ADAD—H⋯A
N2—H5⋯O2i0.90 (2)2.03 (2)2.9155 (19)169.0 (18)
N1—H6⋯O2ii0.98 (2)1.790 (19)2.7565 (18)170.3 (19)
N2—H7⋯O1ii0.92 (2)1.99 (2)2.8976 (19)168.1 (19)
N3—H9⋯O1Wiii0.89 (2)2.09 (2)2.978 (2)179 (3)
N3—H10⋯O2i0.89 (2)2.23 (2)3.078 (2)158.8 (17)
O1W—H11⋯O1iv0.95 (3)1.86 (3)2.7878 (18)165 (3)
O1W—H12⋯O1v0.92 (2)1.99 (2)2.8641 (18)158.2 (19)
C3—H2⋯O1Wvi0.984 (17)2.516 (18)3.369 (2)145.0 (14)
C4—H8⋯Cg1iii1.01 (2)2.76 (2)3.629 (2)144.3 (15)
C6—H3⋯Cg2vii0.959 (18)2.568 (18)3.497 (2)163.4 (14)

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) ; (vii) .

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1.  A short history of SHELX.

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

2.  2-Aminopyridinium salicylate.

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

3.  2-Amino-5-chloro-pyridinium 2-carb-oxy-acetate.

Authors:  Madhukar Hemamalini; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-05-29

4.  2-Amino-5-methyl-pyridinium 2-carb-oxy-acetate.

Authors:  Madhukar Hemamalini; Hoong-Kun Fun
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2010-05-29

5.  2-Amino-5-chloro-pyridinium salicylate.

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

6.  Structure validation in chemical crystallography.

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

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