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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 69| Part 5| May 2013| Page o670
https://doi.org/10.1107/S1600536813008763

3,4-Di­amino­pyridinium hydrogen malonate

Surendra Thapa,a* Sergiu Draguta,b Bhupinder Sandhu,b Mikhail Yu. Antipinb and Tatiana V. Timofeevab

aKathmandu University Budol, Dhulikhel 45200, Nepal, and bDepartment of Chemistry & Biology, New Mexico Highlands University, 803 University Avenue, Las Vegas, NM 87701, USA
*Correspondence e-mail: surenthapa86@gmail.com

(Received 8 March 2013; accepted 30 March 2013; online 10 April 2013)

In the title salt, C5H8N3+·C3H3O4−, the 3,4-di­amino­pyridinium cation is almost planar, with an r.m.s. deviation of 0.02 Å. The conformation of the hydrogen malonate anion is stabilized by an intra­molecular O—H⋯O hydrogen bond, which generates an S(6) ring. In the crystal, N—H⋯O hydrogen bonds link cations and anions into layers parallel to the ab plane.

Related literature

For applications of 3,4-di­amino­pyridine, see: Maddison et al. (2001[Maddison, P., Lang, B., Mills, K. & Newsom-Davis, J. (2001). J. Neurol. Neurosurg. Psychiatry, 70, 212-217.]); Argov (2009[Argov, Z. (2009). Curr. Opin. Neurol. 22, 493-496.]). For related structures, see: De Cires-Mejias et al. (2004[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.]); Koleva et al. (2007[Koleva, B., Tsanev, T., Kolev, T., Mayer-Figge, H. & Sheldrick, W. S. (2007). Acta Cryst. E63, o3356.], 2008[Koleva, B., Kolev, T., Tsanev, T., Kotov, S., Mayer-Figge, H., Seidel, R. W. & Sheldrich, W. S. (2008). J. Mol. Struct. 881, 146-155.]); Fun & Balasubramani (2009[Fun, H.-K. & Balasubramani, K. (2009). Acta Cryst. E65, o1531-o1532.]). For graph-set notation, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data

  • C5H8N3+·C3H3O4−

  • Mr = 213.20

  • Monoclinic, P 21

  • a = 8.7761 (18) Å

  • b = 5.088 (1) Å

  • c = 10.636 (2) Å

  • β = 101.381 (4)°

  • V = 465.58 (17) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.12 mm−1

  • T = 296 K

  • 0.30 × 0.20 × 0.20 mm
Data collection

  • Bruker APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.964, Tmax = 0.976

  • 3498 measured reflections

  • 1248 independent reflections

  • 1066 reflections with I > 2σ(I)

  • Rint = 0.026
Refinement

  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 0.102

  • S = 1.18

  • 1248 reflections

  • 140 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.19 e Å−3

  • Δρmin = −0.15 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1A⋯O3 0.86 1.93 2.784 (3) 175
N2—H2A⋯O1i 0.86 2.28 3.132 (3) 174
N2—H2B⋯O1ii 0.86 2.15 3.005 (3) 176
N3—H3A⋯O2iii 0.86 2.28 3.048 (3) 149
N3—H3B⋯O1ii 0.86 2.10 2.960 (3) 177
O4—H4⋯O2 0.91 (3) 1.55 (3) 2.442 (3) 164 (3)
Symmetry codes: (i) [-x+1, y+{\script{3\over 2}}, -z]; (ii) x-1, y+2, z; (iii) [-x+1, y+{\script{3\over 2}}, -z+1].

Data collection: APEX2 (Bruker, 2005[Bruker (2005). APEX2 Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2001[Bruker (2001). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536813008763/cv5392sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536813008763/cv5392Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536813008763/cv5392Isup3.cml

checkCIF report


Comment top

3,4-Diaminopyridine is used for the treatment of Lambert-Eaton myasthenic syndrome (LEMS) which significantly improve the primary endpoint of muscle strength score, or myometric limb measurement following treatment (Maddison et al. 2001). It is also used to treat many of the congenital myasthenic syndromes (Argov, 2009). The crystal structures of adducts of 3,4-diaminopyridine with different acids such as succinic (Fun et al., 2009), tartaric (Koleva et al., 2008) and squaric acid (Koleva et al., 2007) have been reported in the literature. Herewith we present the crystal structure of the title compound (I).

In (I) (Fig 1), the asymmetric unit consists of a 3,4-diaminopyridinium cation and a hydrogen malonate anion. In the 3,4-diaminopyridinium cation, endocyclic angles cover the range 117.98 (18)–121.95 (18)°. Protonation at atom N1 has led to slight increase in the C2—N1—C6 angle to 121.32 (2)° compared to that in unprotonated structure (De Cires-Mejias et al., 2004). All non-hydrogen atoms lie within the same plane (r.m.s. deviation is 0.02 Å). The dihedral angle between the pyridine ring and the plane formed by the malonic acid molecule is 5.08 (6) °. Hydrogen malonate anion is stabilized by intramolecular O4—H···O2 hydrogen bond.

In the crystal, the protonated N1 atom is bonded to the carboxylate oxygen atom O3 through N—H···O hydrogen bond. The two amino groups (N2 and N3) are involved in the hydrogen bonding via N—H···O H-bonds with hydrogen malonate oxygen atom (O1) to form an R12(7) ring motif (Bernstein et al., 1995). The N3 amino group is hydrogen-bonded to the carboxylate oxygen atom (O3). The N—H···O hydrogen bonds (Table 1) link cations and anions into layers parallel to ab plane (Fig. 2).

Related literature top

For applications of 3,4-diaminopyridine, see: Maddison et al. (2001); Argov (2009). For related structures, see: De Cires-Mejias et al. (2004); Koleva et al. (2007, 2008); Fun & Balasubramani (2009). For graph-set notation, see: Bernstein et al. (1995).

Experimental top

The initial compounds were obtained commercially (Aldrich) as fine-crystalline powders and purified additionally by filtration. 0.003 g (0.028 mmol) of malonic acid and 0.0035 (0.032 mmol) of 3,4 diaminopyridine were disolved in hot ethanol. Crystals suitable for the X-ray diffraction study were obtained after couple of days by slow evaporation (m.p.:130–135°C).

Refinement top

The hydrogen atom of hydroxyl group was localized in the difference-Fourier map and refined isotropically. The other hydrogen atoms were placed in the calculated positions with N—H = 0.86 Å, C—H = 0.93 Å (aromatic) and C—H = 0.97 Å (methylene) and refined in the riding model with fixed isotropic displacement parameters [Uiso(H) = 1.2Ueq(N), Uiso(H) = 1.2Ueq(C)]. In the absence of any significant anomalous scatterers, the 369 Friedel pairs were merged before the final refinement.

Structure description top

3,4-Diaminopyridine is used for the treatment of Lambert-Eaton myasthenic syndrome (LEMS) which significantly improve the primary endpoint of muscle strength score, or myometric limb measurement following treatment (Maddison et al. 2001). It is also used to treat many of the congenital myasthenic syndromes (Argov, 2009). The crystal structures of adducts of 3,4-diaminopyridine with different acids such as succinic (Fun et al., 2009), tartaric (Koleva et al., 2008) and squaric acid (Koleva et al., 2007) have been reported in the literature. Herewith we present the crystal structure of the title compound (I).

In (I) (Fig 1), the asymmetric unit consists of a 3,4-diaminopyridinium cation and a hydrogen malonate anion. In the 3,4-diaminopyridinium cation, endocyclic angles cover the range 117.98 (18)–121.95 (18)°. Protonation at atom N1 has led to slight increase in the C2—N1—C6 angle to 121.32 (2)° compared to that in unprotonated structure (De Cires-Mejias et al., 2004). All non-hydrogen atoms lie within the same plane (r.m.s. deviation is 0.02 Å). The dihedral angle between the pyridine ring and the plane formed by the malonic acid molecule is 5.08 (6) °. Hydrogen malonate anion is stabilized by intramolecular O4—H···O2 hydrogen bond.

In the crystal, the protonated N1 atom is bonded to the carboxylate oxygen atom O3 through N—H···O hydrogen bond. The two amino groups (N2 and N3) are involved in the hydrogen bonding via N—H···O H-bonds with hydrogen malonate oxygen atom (O1) to form an R12(7) ring motif (Bernstein et al., 1995). The N3 amino group is hydrogen-bonded to the carboxylate oxygen atom (O3). The N—H···O hydrogen bonds (Table 1) link cations and anions into layers parallel to ab plane (Fig. 2).

For applications of 3,4-diaminopyridine, see: Maddison et al. (2001); Argov (2009). For related structures, see: De Cires-Mejias et al. (2004); Koleva et al. (2007, 2008); Fun & Balasubramani (2009). For graph-set notation, see: Bernstein et al. (1995).

Computing details top

Data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The content of asymmetric unit of I showing the atomic numbering and hydrogen bonds as dashed lines. Displacement ellipsoids are drawn at the 50% probability level. H atoms are presented as small spheres of arbitrary radius.
[Figure 2] Fig. 2. A portion of the crystal packing viewed approximately down the b axis and showing intermolecular N—H···O hydrogen bonds as dashed lines.
3,4-Diaminopyridinium 2-carboxyethanoate top
Crystal data top
C5H8N3+·C3H3O4−F(000) = 224
Mr = 213.20Dx = 1.521 Mg m−3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 1070 reflections
a = 8.7761 (18) Åθ = 2.8–27.0°
b = 5.088 (1) ŵ = 0.12 mm−1
c = 10.636 (2) ÅT = 296 K
β = 101.381 (4)°Prism, colourless
V = 465.58 (17) Å30.30 × 0.20 × 0.20 mm
Z = 2
Data collection top
Bruker APEXII CCD
diffractometer		1248 independent reflections
Radiation source: fine-focus sealed tube1066 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.026
φ and ω scansθmax = 28.0°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)		h = −11→11
Tmin = 0.964, Tmax = 0.976k = −6→6
3498 measured reflectionsl = −14→14
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.102H atoms treated by a mixture of independent and constrained refinement
S = 1.18 w = 1/[σ2(Fo2) + (0.0456P)2 + 0.0455P]
where P = (Fo2 + 2Fc2)/3
1248 reflections(Δ/σ)max < 0.001
140 parametersΔρmax = 0.19 e Å−3
1 restraintΔρmin = −0.15 e Å−3
Crystal data top
C5H8N3+·C3H3O4−V = 465.58 (17) Å3
Mr = 213.20Z = 2
Monoclinic, P21Mo Kα radiation
a = 8.7761 (18) ŵ = 0.12 mm−1
b = 5.088 (1) ÅT = 296 K
c = 10.636 (2) Å0.30 × 0.20 × 0.20 mm
β = 101.381 (4)°
Data collection top
Bruker APEXII CCD
diffractometer		1248 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)		1066 reflections with I > 2σ(I)
Tmin = 0.964, Tmax = 0.976Rint = 0.026
3498 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0401 restraint
wR(F2) = 0.102H atoms treated by a mixture of independent and constrained refinement
S = 1.18Δρmax = 0.19 e Å−3
1248 reflectionsΔρmin = −0.15 e Å−3
140 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.3630 (3)0.6491 (5)0.2325 (2)0.0467 (6)
H1A0.41980.53290.20520.056*
N20.0891 (3)1.1609 (5)0.09714 (19)0.0461 (6)
H2A0.09221.14900.01700.055*
H2B0.02831.27300.12250.055*
N30.0818 (3)1.1851 (5)0.3616 (2)0.0428 (5)
H3A0.07921.18940.44200.051*
H3B0.02531.29170.30940.051*
C20.2794 (3)0.8205 (5)0.1477 (3)0.0422 (6)
H20.28930.81470.06230.051*
C30.1811 (3)1.0013 (5)0.1844 (2)0.0333 (5)
C40.1737 (3)1.0129 (5)0.3178 (2)0.0335 (5)
C50.2662 (3)0.8383 (6)0.4014 (3)0.0423 (6)
H50.26490.84500.48860.051*
C60.3587 (3)0.6579 (6)0.3574 (3)0.0485 (7)
H60.41840.54160.41420.058*
O10.8907 (2)−0.4299 (4)0.19036 (19)0.0501 (5)
O20.7898 (2)−0.2740 (5)0.35111 (17)0.0536 (6)
O30.5470 (2)0.2937 (4)0.13031 (19)0.0483 (5)
O40.6154 (3)0.1047 (4)0.32045 (18)0.0494 (5)
H40.674 (4)−0.042 (7)0.345 (3)0.044 (9)*
C70.8059 (3)−0.2775 (5)0.2335 (2)0.0356 (6)
C80.7139 (3)−0.0761 (5)0.1443 (2)0.0340 (5)
H8A0.78650.01920.10340.041*
H8B0.6444−0.17110.07740.041*
C90.6182 (3)0.1235 (5)0.1993 (2)0.0348 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0438 (12)0.0339 (12)0.0626 (14)0.0032 (11)0.0108 (10)−0.0094 (12)
N20.0563 (13)0.0490 (14)0.0309 (10)0.0087 (12)0.0035 (9)0.0022 (10)
N30.0515 (12)0.0438 (13)0.0325 (10)0.0068 (11)0.0071 (9)−0.0015 (10)
C20.0424 (14)0.0394 (15)0.0431 (13)−0.0060 (13)0.0043 (11)−0.0061 (12)
C30.0334 (12)0.0334 (13)0.0324 (11)−0.0062 (11)0.0043 (9)−0.0017 (10)
C40.0359 (12)0.0296 (12)0.0337 (11)−0.0025 (11)0.0039 (9)−0.0014 (10)
C50.0464 (14)0.0396 (15)0.0374 (12)0.0013 (13)0.0002 (11)0.0068 (11)
C60.0493 (16)0.0365 (14)0.0565 (16)0.0019 (13)0.0027 (12)0.0082 (14)
O10.0502 (11)0.0430 (12)0.0555 (11)0.0150 (10)0.0066 (9)0.0097 (10)
O20.0702 (14)0.0551 (13)0.0323 (9)−0.0030 (11)0.0025 (8)0.0095 (9)
O30.0470 (11)0.0402 (11)0.0558 (11)0.0132 (9)0.0055 (8)−0.0025 (9)
O40.0606 (12)0.0508 (13)0.0380 (10)0.0003 (12)0.0129 (9)−0.0113 (10)
C70.0361 (13)0.0345 (13)0.0340 (12)−0.0029 (11)0.0014 (9)0.0048 (11)
C80.0381 (12)0.0363 (13)0.0268 (10)0.0051 (11)0.0044 (9)0.0028 (10)
C90.0328 (12)0.0346 (13)0.0363 (11)−0.0054 (11)0.0053 (9)−0.0038 (11)
Geometric parameters (Å, º) top
N1—C61.337 (4)C5—C61.368 (4)
N1—C21.360 (4)C5—H50.9300
N1—H1A0.8600C6—H60.9300
N2—C31.370 (3)O1—C71.225 (3)
N2—H2A0.8600O2—C71.286 (3)
N2—H2B0.8600O3—C91.224 (3)
N3—C41.335 (3)O4—C91.298 (3)
N3—H3A0.8600O4—H40.91 (3)
N3—H3B0.8600C7—C81.517 (3)
C2—C31.369 (4)C8—C91.507 (3)
C2—H20.9300C8—H8A0.9700
C3—C41.435 (3)C8—H8B0.9700
C4—C51.398 (3)
C6—N1—C2121.3 (3)C6—C5—H5119.4
C6—N1—H1A119.4C4—C5—H5119.4
C2—N1—H1A119.4N1—C6—C5119.9 (3)
C3—N2—H2A120.0N1—C6—H6120.1
C3—N2—H2B120.0C5—C6—H6120.1
H2A—N2—H2B120.0C9—O4—H4102.8 (19)
C4—N3—H3A120.0O1—C7—O2124.4 (2)
C4—N3—H3B120.0O1—C7—C8118.7 (2)
H3A—N3—H3B120.0O2—C7—C8116.9 (2)
N1—C2—C3122.0 (2)C9—C8—C7118.75 (19)
N1—C2—H2119.0C9—C8—H8A107.6
C3—C2—H2119.0C7—C8—H8A107.6
C2—C3—N2121.7 (2)C9—C8—H8B107.6
C2—C3—C4117.6 (2)C7—C8—H8B107.6
N2—C3—C4120.7 (2)H8A—C8—H8B107.1
N3—C4—C5120.7 (2)O3—C9—O4122.7 (2)
N3—C4—C3121.4 (2)O3—C9—C8120.1 (2)
C5—C4—C3118.0 (2)O4—C9—C8117.2 (2)
C6—C5—C4121.2 (2)
C6—N1—C2—C3−3.3 (4)C3—C4—C5—C6−1.4 (4)
N1—C2—C3—N2−175.4 (3)C2—N1—C6—C51.4 (4)
N1—C2—C3—C42.7 (4)C4—C5—C6—N10.9 (4)
C2—C3—C4—N3179.4 (3)O1—C7—C8—C9−175.8 (2)
N2—C3—C4—N3−2.5 (4)O2—C7—C8—C93.6 (4)
C2—C3—C4—C5−0.4 (3)C7—C8—C9—O3177.5 (2)
N2—C3—C4—C5177.7 (2)C7—C8—C9—O4−2.7 (3)
N3—C4—C5—C6178.8 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O30.861.932.784 (3)175
N2—H2A···O1i0.862.283.132 (3)174
N2—H2B···O1ii0.862.153.005 (3)176
N3—H3A···O2iii0.862.283.048 (3)149
N3—H3B···O1ii0.862.102.960 (3)177
O4—H4···O20.91 (3)1.55 (3)2.442 (3)164 (3)
Symmetry codes: (i) −x+1, y+3/2, −z; (ii) x−1, y+2, z; (iii) −x+1, y+3/2, −z+1.

Experimental details

Crystal data
Chemical formulaC5H8N3+·C3H3O4−
Mr213.20
Crystal system, space groupMonoclinic, P21
Temperature (K)296
a, b, c (Å)8.7761 (18), 5.088 (1), 10.636 (2)
β (°) 101.381 (4)
V (Å3)465.58 (17)
Z2
Radiation typeMo Kα
µ (mm−1)0.12
Crystal size (mm)0.30 × 0.20 × 0.20
Data collection
DiffractometerBruker APEXII CCD
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.964, 0.976
No. of measured, independent and
observed [I > 2σ(I)] reflections		3498, 1248, 1066
Rint0.026
(sin θ/λ)max (Å−1)0.661
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.102, 1.18
No. of reflections1248
No. of parameters140
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.19, −0.15

Computer programs: APEX2 (Bruker, 2005), SAINT (Bruker, 2001), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1A···O30.861.932.784 (3)174.6
N2—H2A···O1i0.862.283.132 (3)173.6
N2—H2B···O1ii0.862.153.005 (3)175.9
N3—H3A···O2iii0.862.283.048 (3)148.6
N3—H3B···O1ii0.862.102.960 (3)176.5
O4—H4···O20.91 (3)1.55 (3)2.442 (3)164 (3)
Symmetry codes: (i) −x+1, y+3/2, −z; (ii) x−1, y+2, z; (iii) −x+1, y+3/2, −z+1.
 

Acknowledgements

The authors are grateful for NSF support via grants DMR 0934212 (PREM) and CHE 0832622.

References

First citationArgov, Z. (2009). Curr. Opin. Neurol. 22, 493–496.  Web of Science CrossRef PubMed Google Scholar
 First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
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ISSN: 2056-9890
Volume 69| Part 5| May 2013| Page o670
https://doi.org/10.1107/S1600536813008763
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