PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o1854–o1855.
Published online 2009 July 15. doi:  10.1107/S1600536809026439
PMCID: PMC2977310

Bis(2,3-diamino­pyridinium) succinate trihydrate

Abstract

In the title salt, 2C5H8N3 +·C4H4O4 2−·3H2O, the asymmetric unit contains a protonated 2,3-diamino­pyridinium cation, half of a succinate dianion (disposed about a centre of inversion), and one and a half water mol­ecules. One of the water mol­ecules is disordered over two sites with occupancies of 0.670 (17) and 0.330 (17). The other water mol­ecule has an occupancy of 0.5 (from refinement). The pyridine N atom of the 2,3-diamino­pyridine mol­ecule is protonated. The protonated N atom and one of the 2-amino H atoms are hydrogen bonded to the succinate anion through a pair of N—H(...)O hydrogen bonds, forming an R 2 2(8) ring motif. In the crystal, mol­ecules are consolidated into a three-dimensional network by N—H(...)O and O—H(...)O inter­actions.

Related literature

For substituted pyridines, see: Pozharski et al. (1997 [triangle]); Katritzky et al. (1996 [triangle]); Jeffrey & Saenger (1991 [triangle]); Jeffrey (1997 [triangle]); Scheiner (1997 [triangle]). For related structures, see: De Cires-Mejias et al. (2004 [triangle]); Fun & Balasubramani (2009 [triangle]); Balasubramani & Fun (2009a [triangle],b [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1854-scheme1.jpg

Experimental

Crystal data

  • 2C5H8N3 +·C4H4O4 2−·3H2O
  • M r = 195.20
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1854-efi1.jpg
  • a = 12.7159 (4) Å
  • b = 3.9024 (1) Å
  • c = 18.7734 (6) Å
  • β = 94.933 (2)°
  • V = 928.13 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 100 K
  • 0.17 × 0.13 × 0.06 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.981, T max = 0.993
  • 10934 measured reflections
  • 2121 independent reflections
  • 1364 reflections with I > 2σ(I)
  • R int = 0.056

Refinement

  • R[F 2 > 2σ(F 2)] = 0.062
  • wR(F 2) = 0.129
  • S = 1.06
  • 2121 reflections
  • 178 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.26 e Å−3
  • Δρmin = −0.24 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809026439/tk2489sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809026439/tk2489Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

HKF and KBS thank the Malaysian Government and Universiti Sains Malaysia for Science Fund grant No. 305/PFIZIK/613312. KBS thanks Universiti Sains Malaysia for a post–doctoral research fellowship. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012.

supplementary crystallographic information

Comment

Pyridine and its derivatives play an important role in heterocyclic chemistry (Pozharski et al., 1997; Katritzky et al., 1996). Further, pyridine and its substituted derivatives are often involved in hydrogen-bond interactions (Jeffrey & Saenger, 1991; Jeffrey, 1997;Scheiner, 1997). The crystal structures of 2,3-diaminopyridinium 4-hydroxybenzoate (Fun & Balasubramani, 2009), 2,3-diaminopyridinium 4-nitrobenzoate (Balasubramani & Fun, 2009a) and 2,3-diaminopyridinium benzoate (Balasubramani & Fun, 2009b) have been reported by us recently. In the hope to study some interesting hydrogen-bonding interactions, the title compound (I) was synthesized. Its molecular and crystal structure is presented here.

The asymmetric unit of (I) (Fig. 1), contains a protonated 2,3-diaminopyridinium cation, a half molecule of succinate anion (disposed about a centre of inversion), and one and half water molecules. In the 2,3-diaminopyridinium cation, protonatation N1 atom has lead to a slight increase (ca. 4 °) in the C1—N1—C5 angle to 123.6 (2)° compared with the unprotonated structure (De Cires-Mejias et al., 2004). The 2,3-diaminopyridinium cation is planar, with a maximum deviation of 0.004 (2) Å for atom C2.

In the crystal packing (Fig. 2), the protonated N1 atom and a nitrogen atom of the 2-amino group (N2) are hydrogen-bonded to the succinate oxygen atoms (O2 and O1) via a pair of N—H···O hydrogen bonds forming a ring motif R22(8) (Bernstein et al., 1995). The 2-amino groups (N2 and N3) are involved in N—H···O hydrogen-bonding interactions to form a R21(7) ring motif. The crystal structure is further stabilized by water molecules via O(water)—H···O and N—H···O(water) hydrogen bonding (Table 1 and Fig. 2).

Experimental

An aqueous solution of hot methanol (10 ml/ 10 ml) of 2,3-diaminopyridine (27 mg, Aldrich) and succinic acid (29 mg, Merck) were mixed and warmed over a heating magnetic stirrer for 5 minutes. The resulting solution was allowed to cool slowly at room temperature. Crystals of (I) appeared from the mother liquor after a few days.

Refinement

All the H atoms (other than the water H-atoms) were located from the difference Fourier map and allowed to refine freely [N–H = 0.85 (3)–0.96 (3) Å & C–H = 0.93 (2)–0.98 (2) Å]. The water H-atoms were located from the difference Fourier map but constrained to 0.85 Å from the parent atom with Uiso(H) = 1.5Ueq(O).

One water molecule has a refined occupancy of 0.495 (7) which was then fixed as 0.5 in the final refinement. The other water molecule is disordered (O1WA & O1WB) over two sites with occupancies of 0.670 (17) and 0.330 (17).

Figures

Fig. 1.
The molecular structure of (I), showing 50% probability displacement ellipsoids and the atom numbering scheme. Dashed lines indicate the hydrogen bonding. The O1 water molecule is disordered over two positions. Symmetry operation A:-x, 2-y, 1-z.
Fig. 2.
Part of the crystal packing showing the overall 3-D hydrogen-bonding network in (I). Dashed lines indicate the hydrogen bonding.

Crystal data

2C5H8N3+·C4H4O42·3H2OF(000) = 416
Mr = 195.20Dx = 1.397 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2108 reflections
a = 12.7159 (4) Åθ = 2.2–30.0°
b = 3.9024 (1) ŵ = 0.11 mm1
c = 18.7734 (6) ÅT = 100 K
β = 94.933 (2)°Block, brown
V = 928.13 (5) Å30.17 × 0.13 × 0.06 mm
Z = 4

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2121 independent reflections
Radiation source: fine-focus sealed tube1364 reflections with I > 2σ(I)
graphiteRint = 0.056
[var phi] and ω scansθmax = 27.5°, θmin = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −16→16
Tmin = 0.981, Tmax = 0.993k = −4→5
10934 measured reflectionsl = −24→21

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.062Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.129H atoms treated by a mixture of independent and constrained refinement
S = 1.06w = 1/[σ2(Fo2) + (0.041P)2 + 0.7373P] where P = (Fo2 + 2Fc2)/3
2121 reflections(Δ/σ)max < 0.001
178 parametersΔρmax = 0.26 e Å3
0 restraintsΔρmin = −0.24 e Å3

Special details

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 > 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/UeqOcc. (<1)
O10.02464 (12)0.7567 (4)0.37851 (8)0.0251 (4)
O20.18198 (12)0.6548 (5)0.43615 (8)0.0264 (4)
N10.25383 (14)0.2963 (5)0.33114 (10)0.0204 (5)
N20.10876 (15)0.4334 (6)0.25459 (12)0.0243 (5)
N30.20743 (19)0.1167 (7)0.14153 (12)0.0328 (6)
C10.20422 (17)0.2863 (6)0.26523 (12)0.0201 (5)
C20.25526 (17)0.1188 (6)0.20981 (12)0.0221 (6)
C30.35320 (18)−0.0256 (7)0.22796 (13)0.0243 (6)
C40.40151 (18)−0.0059 (7)0.29740 (13)0.0248 (6)
C50.35068 (18)0.1562 (7)0.34840 (13)0.0241 (6)
C60.08824 (17)0.7727 (6)0.43321 (12)0.0207 (5)
C70.05630 (18)0.9358 (7)0.50147 (12)0.0207 (5)
O1WA0.3424 (4)0.840 (3)0.5375 (3)0.082 (3)0.670 (17)
H1WA0.38030.66250.53410.123*0.670 (17)
H2WA0.28980.82220.50660.123*0.670 (17)
O1WB0.3443 (6)0.583 (4)0.5327 (3)0.039 (4)0.330 (17)
H1WB0.33120.79540.53650.058*0.330 (17)
H2WB0.31730.51820.49190.058*0.330 (17)
O2W0.4593 (3)0.248 (2)0.5467 (3)0.110 (3)0.50
H1W20.51190.35430.53220.165*0.50
H2W20.44620.07940.51870.165*0.50
H4A0.4676 (19)−0.100 (7)0.3090 (12)0.027 (7)*
H5A0.3781 (17)0.185 (6)0.3960 (13)0.022 (6)*
H3A0.3854 (18)−0.140 (7)0.1902 (13)0.030 (7)*
H7B0.0722 (17)0.759 (6)0.5381 (12)0.020 (6)*
H7A0.1062 (18)1.118 (7)0.5145 (12)0.026 (7)*
H2N20.076 (2)0.445 (8)0.2102 (16)0.047 (9)*
H1N30.142 (2)0.154 (7)0.1337 (14)0.037 (8)*
H1N20.0799 (19)0.537 (7)0.2905 (14)0.028 (7)*
H2N30.239 (2)−0.022 (8)0.1105 (15)0.045 (9)*
H1N10.2213 (19)0.418 (7)0.3676 (13)0.030 (7)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0211 (8)0.0345 (11)0.0203 (8)0.0028 (8)0.0054 (7)−0.0005 (7)
O20.0188 (8)0.0361 (11)0.0253 (9)0.0030 (8)0.0074 (7)−0.0010 (8)
N10.0177 (10)0.0213 (12)0.0235 (10)−0.0029 (9)0.0084 (8)−0.0007 (9)
N20.0203 (11)0.0296 (13)0.0239 (11)0.0020 (10)0.0066 (9)−0.0041 (10)
N30.0263 (13)0.0450 (16)0.0277 (12)0.0052 (12)0.0056 (10)−0.0071 (11)
C10.0172 (11)0.0179 (13)0.0259 (12)−0.0052 (10)0.0067 (9)0.0016 (10)
C20.0219 (12)0.0213 (14)0.0242 (12)−0.0050 (11)0.0074 (10)−0.0006 (10)
C30.0229 (12)0.0215 (15)0.0304 (13)−0.0033 (11)0.0134 (10)−0.0025 (11)
C40.0153 (12)0.0234 (14)0.0366 (14)−0.0026 (11)0.0067 (10)0.0008 (12)
C50.0204 (12)0.0251 (15)0.0269 (13)−0.0031 (11)0.0028 (10)0.0024 (11)
C60.0219 (12)0.0185 (14)0.0229 (12)−0.0022 (11)0.0082 (10)0.0049 (10)
C70.0207 (12)0.0212 (14)0.0204 (12)−0.0003 (11)0.0035 (10)0.0027 (11)
O1WA0.068 (3)0.111 (8)0.061 (3)−0.030 (3)−0.026 (2)0.022 (3)
O1WB0.031 (4)0.064 (9)0.020 (3)0.009 (4)−0.002 (2)−0.009 (3)
O2W0.039 (3)0.210 (8)0.078 (4)−0.015 (4)−0.016 (3)−0.006 (4)

Geometric parameters (Å, °)

O1—C61.253 (3)C4—H4A0.93 (2)
O2—C61.274 (3)C5—H5A0.94 (2)
N1—C11.340 (3)C6—C71.517 (3)
N1—C51.361 (3)C7—C7i1.513 (4)
N1—H1N10.96 (3)C7—H7B0.98 (2)
N2—C11.342 (3)C7—H7A0.97 (3)
N2—H2N20.90 (3)O1WA—H1WA0.8500
N2—H1N20.89 (3)O1WA—H2WA0.8501
N3—C21.371 (3)O1WA—H1WB0.2257
N3—H1N30.85 (3)O1WB—H1WA0.5518
N3—H2N30.91 (3)O1WB—H2WA1.2381
C1—C21.431 (3)O1WB—H1WB0.8500
C2—C31.383 (3)O1WB—H2WB0.8502
C3—C41.395 (3)O2W—H1W20.8500
C3—H3A0.96 (3)O2W—H2W20.8501
C4—C51.357 (3)
C1—N1—C5123.6 (2)C4—C5—H5A124.5 (14)
C1—N1—H1N1118.5 (14)N1—C5—H5A115.7 (14)
C5—N1—H1N1117.9 (14)O1—C6—O2123.6 (2)
C1—N2—H2N2120.3 (18)O1—C6—C7120.8 (2)
C1—N2—H1N2120.5 (15)O2—C6—C7115.61 (19)
H2N2—N2—H1N2119 (2)C7i—C7—C6115.4 (2)
C2—N3—H1N3120.8 (18)C7i—C7—H7B113.3 (13)
C2—N3—H2N3114.7 (17)C6—C7—H7B104.0 (13)
H1N3—N3—H2N3118 (3)C7i—C7—H7A111.3 (14)
N1—C1—N2118.2 (2)C6—C7—H7A107.7 (14)
N1—C1—C2118.5 (2)H7B—C7—H7A104.4 (18)
N2—C1—C2123.2 (2)H1WA—O1WA—H2WA107.4
N3—C2—C3123.1 (2)H1WA—O1WA—H1WB73.7
N3—C2—C1119.4 (2)H2WA—O1WA—H1WB54.6
C3—C2—C1117.5 (2)H1WA—O1WB—H2WA91.7
C2—C3—C4121.5 (2)H1WA—O1WB—H1WB67.4
C2—C3—H3A116.1 (14)H2WA—O1WB—H1WB35.9
C4—C3—H3A122.3 (14)H1WA—O1WB—H2WB118.6
C5—C4—C3119.1 (2)H2WA—O1WB—H2WB72.5
C5—C4—H4A119.8 (15)H1WB—O1WB—H2WB107.4
C3—C4—H4A121.1 (15)H1W2—O2W—H2W2107.4
C4—C5—N1119.7 (2)
C5—N1—C1—N2180.0 (2)C1—C2—C3—C4−0.8 (4)
C5—N1—C1—C20.2 (3)C2—C3—C4—C50.6 (4)
N1—C1—C2—N3−177.7 (2)C3—C4—C5—N10.0 (4)
N2—C1—C2—N32.6 (4)C1—N1—C5—C4−0.4 (4)
N1—C1—C2—C30.4 (3)O1—C6—C7—C7i1.6 (4)
N2—C1—C2—C3−179.4 (2)O2—C6—C7—C7i−177.9 (3)
N3—C2—C3—C4177.2 (2)

Symmetry codes: (i) −x, −y+2, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2N2···O1ii0.90 (3)2.14 (3)2.978 (3)155 (3)
N3—H1N3···O1ii0.85 (3)2.14 (3)2.993 (3)176 (3)
N3—H2N3···O1WAiii0.91 (3)2.34 (3)3.243 (6)172 (2)
O1WA—H2WA···O20.851.932.764 (5)165
N2—H1N2···O10.89 (3)2.04 (3)2.929 (3)175 (2)
N1—H1N1···O20.96 (3)1.69 (3)2.643 (3)171 (2)

Symmetry codes: (ii) −x, y−1/2, −z+1/2; (iii) x, −y+1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2489).

References

  • Balasubramani, K. & Fun, H.-K. (2009a). Acta Cryst. E65, o1511–o1512. [PMC free article] [PubMed]
  • Balasubramani, K. & Fun, H.-K. (2009b). Acta Cryst. E65, o1519. [PMC free article] [PubMed]
  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
  • Bruker (2005). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  • De Cires-Mejias, C., Tanase, S., Reedijk, J., Gonzalez-Vilchez, F., Vilaplana, R., Mills, A. M., Kooijman, H. & Spek, A. L. (2004). Inorg. Chim. Acta, 357, 1494–1498.
  • Fun, H.-K. & Balasubramani, K. (2009). Acta Cryst. E65, o1496–o1497. [PMC free article] [PubMed]
  • Jeffrey, G. A. (1997). An Introduction to Hydrogen Bonding Oxford University Press.
  • Jeffrey, G. A. & Saenger, W. (1991). Hydrogen Bonding in Biological Structures Berlin: Springer.
  • Katritzky, A. R., Rees, C. W. & Scriven, E. F. V. (1996). Comprehensive Heterocyclic Chemistry II Oxford: Pergamon Press.
  • Pozharski, A. F., Soldatenkov, A. T. & Katritzky, A. R. (1997). Heterocycles in Life and Society New York: Wiley.
  • Scheiner, S. (1997). Hydrogen Bonding, A Theoretical Perspective Oxford University Press.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography