2-Amino-5-methyl­pyridinium nitrate

Yan, X.; Fan, Y.; Bi, C.; Zuo, J.; Zhang, Z.

doi:10.1107/S1600536812025196

organic compounds

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ISSN: 2056-9890

Volume 68| Part 7| July 2012| Page o2084

https://doi.org/10.1107/S1600536812025196

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2-Amino-5-methylpyridinium nitrate

Xingchen Yan,^a Yuhua Fan,^a ^* Caifeng Bi,^a Jian Zuo ^a and Zhongyu Zhang ^a

^aKey Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, Shandong 266100, People's Republic of China
^*Correspondence e-mail: fanyuhua301@163.com

(Received 22 May 2012; accepted 2 June 2012; online 13 June 2012)

In the title salt, C₆H₉N₂⁺·NO₃⁻, the 2-amino-5-methylpyridinium cation and the nitrate anion are cyclically linked through pyridinium and amine N—H⋯O hydrogen bonds [graph set R₄³(12)]. These units are extended into a zigzag chain structure lying parallel to the a axis, through a second cyclic R₂²(8) association involving amine N—H⋯O and aromatic C—H⋯O hydrogen bonds to nitrate O-atom acceptors.

Related literature

For supramolecular architectures, see: Wang et al. (2012 ). For the potential of amine derivatives to form metal-organic frameworks, see: Manzur et al. (2007 ); Ismayilov et al. (2007 ); Austria et al. (2007 ). For related structures, see: Nahringbauer & Kvick (1977 ); Sherfinski & Marsh (1975 ); Zaouali Zgolli et al. (2009 ); Dai (2008 ). For graph-set analysis, see: Etter et al. (1990 ).

Experimental

Crystal data

C₆H₉N₂⁺·NO₃⁻
M_r = 171.16
Monoclinic, C c
a = 8.7711 (7) Å
b = 15.7261 (13) Å
c = 6.8539 (5) Å
β = 117.455 (2)°
V = 838.92 (12) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 298 K
0.49 × 0.38 × 0.21 mm

Data collection

Bruker SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.948, T_max = 0.977
2040 measured reflections
1251 independent reflections
1077 reflections with I > 2σ(I)
R_int = 0.031

Refinement

R[F² > 2σ(F²)] = 0.039
wR(F²) = 0.109
S = 1.08
1251 reflections
111 parameters
2 restraints
H-atom parameters constrained
Δρ_max = 0.15 e Å⁻³
Δρ_min = −0.13 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O2ⁱ	0.86	1.95	2.808 (4)	177
N2—H2A⋯O1	0.86	2.18	2.992 (4)	157
N2—H2B⋯O1ⁱⁱ	0.86	2.12	2.948 (4)	160
C2—H2⋯O3ⁱⁱ	0.93	2.45	3.304 (4)	153
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 2000 ); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536812025196/zs2211sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812025196/zs2211Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812025196/zs2211Isup3.cml

checkCIF report

Comment top

In the area of predictable assembly of supramolecular architectures, more and more attention has been paid to crystals built from various organic components with specific functional groups (Wang et al., 2012). Because derivatives of the amino acids have the biological activity and amine derivatives have potential to form metal-organic frameworks (Manzur et al., 2007; Ismayilov et al., 2007; Austria et al., 2007), compounds having such functional groups have received considerable attention. The crystal structures of the molecules 2-amino-5-methylpyridine (Nahringbauer & Kvick, 1977), 2-amino-5-methylpyridine hydrochloride (Sherfinski & Marsh, 1975), 2-amino-5-chloropyridinium nitrate (Zaouali Zgolli et al., 2009), and 2-amino-5-cyanopyridinium nitrate (Dai, 2008) have been reported in the literature. We report here the single-crystal structure of the title salt, 2-amino-5-methylpyridium nitrate, C₆H₉N₂⁺ . NO₃^-, which was the product obtained in the attempted preparation of a Schiff base Sm^III complex using Sm(NO₃)₃ . 6H₂O.

In the title salt (Fig. 1), the 2-amino-5-methylpyridinium cation and the nitrate anion are cyclically linked through pyridinium and amine N—H···O hydrogen bonds [graph set R³₄(12) (Etter et al., 1990)] (Table 1). These units are extended into a one-dimensional zigzag chain structure lying parallel to the a axis, through a second cyclic R²₂(8) association involving amine N—H···O and aromatic C—H···O hydrogen bonds to nitrate O-acceptors (Fig. 2).

Related literature top

For supramolecular architectures, see: Wang et al. (2012). For metal-organic frameworks involving amine derivatives, see: Manzur et al. (2007); Ismayilov et al. (2007); Austria et al. (2007). For related structures, see: Nahringbauer & Kvick (1977); Sherfinski & Marsh (1975); Zaouali Zgolli et al. (2009); Dai (2008). For graph-set analysis, see: Etter et al. (1990).

Experimental top

2-Amino-5-methylpyridine (0.324 g, 3 mmol) and 1,3-dihydroxyacetone dimer (0.270 g, 1.5 mmol) were dissolved in methanol (10 ml) and this solution was stirred for 6 h at 333 K. Sm(NO₃)₃ . 6H₂O (0.667 g, 1.5 mmol) was then added and the solution was stirred for a further 4 h. This solution was evaporated in air at room temperature, affording pale-yellow needle-shaped crystals suitable for X-ray analysis.

Structure description top

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The structure and atom-numbering scheme of the title compound, showing 30% probability displacement ellipsoids.
	Fig. 2. A view of the packing showing the zigzag chain parallel to the a axis. Hydrogen bonds are shown as dashed lines.

2-Amino-5-methylpyridinium nitrate top

Crystal data top

C₆H₉N₂⁺·NO₃⁻	F(000) = 360
M_r = 171.16	D_x = 1.355 Mg m⁻³
Monoclinic, Cc	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: C -2yc	Cell parameters from 1097 reflections
a = 8.7711 (7) Å	θ = 2.6–25.8°
b = 15.7261 (13) Å	µ = 0.11 mm⁻¹
c = 6.8539 (5) Å	T = 298 K
β = 117.455 (2)°	Needle, light-yellow
V = 838.92 (12) Å³	0.49 × 0.38 × 0.21 mm
Z = 4

Data collection top

Bruker SMART CCD area-detector diffractometer	1251 independent reflections
Radiation source: fine-focus sealed tube	1077 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.031
φ and ω scans	θ_max = 25.0°, θ_min = 2.6°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −10→10
T_min = 0.948, T_max = 0.977	k = −15→18
2040 measured reflections	l = −8→8

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.039	H-atom parameters constrained
wR(F²) = 0.109	w = 1/[σ²(F_o²) + (0.0569P)² + 0.1897P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max < 0.001
1251 reflections	Δρ_max = 0.15 e Å⁻³
111 parameters	Δρ_min = −0.13 e Å⁻³
2 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.010 (3)

Crystal data top

C₆H₉N₂⁺·NO₃⁻	V = 838.92 (12) Å³
M_r = 171.16	Z = 4
Monoclinic, Cc	Mo Kα radiation
a = 8.7711 (7) Å	µ = 0.11 mm⁻¹
b = 15.7261 (13) Å	T = 298 K
c = 6.8539 (5) Å	0.49 × 0.38 × 0.21 mm
β = 117.455 (2)°

Data collection top

Bruker SMART CCD area-detector diffractometer	1251 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	1077 reflections with I > 2σ(I)
T_min = 0.948, T_max = 0.977	R_int = 0.031
2040 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	2 restraints
wR(F²) = 0.109	H-atom parameters constrained
S = 1.08	Δρ_max = 0.15 e Å⁻³
1251 reflections	Δρ_min = −0.13 e Å⁻³
111 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

	x	y	z	U_iso*/U_eq
N1	0.3088 (3)	0.46545 (15)	0.4791 (4)	0.0474 (6)
H1	0.2362	0.4246	0.4239	0.057*
N2	0.5229 (4)	0.36493 (16)	0.6464 (4)	0.0593 (7)
H2A	0.4482	0.3251	0.5882	0.071*
H2B	0.6289	0.3524	0.7293	0.071*
N3	0.4592 (3)	0.14462 (15)	0.6312 (5)	0.0583 (7)
O1	0.3527 (3)	0.19547 (15)	0.5007 (4)	0.0897 (9)
O2	0.5816 (3)	0.17188 (14)	0.8011 (5)	0.0823 (8)
O3	0.4431 (3)	0.06826 (15)	0.5931 (5)	0.0912 (9)
C1	0.4743 (3)	0.44596 (15)	0.6084 (4)	0.0450 (7)
C2	0.5894 (4)	0.51441 (18)	0.6972 (5)	0.0499 (7)
H2	0.7054	0.5042	0.7882	0.060*
C3	0.5302 (4)	0.59519 (18)	0.6493 (5)	0.0534 (8)
H3	0.6077	0.6399	0.7078	0.064*
C4	0.3574 (4)	0.61376 (17)	0.5153 (5)	0.0507 (7)
C5	0.2500 (4)	0.54681 (17)	0.4312 (5)	0.0519 (7)
H5	0.1340	0.5565	0.3390	0.062*
C6	0.2926 (5)	0.7045 (2)	0.4632 (7)	0.0767 (11)
H6A	0.1721	0.7042	0.3623	0.115*
H6B	0.3539	0.7339	0.3982	0.115*
H6C	0.3109	0.7328	0.5963	0.115*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0453 (13)	0.0430 (12)	0.0475 (15)	−0.0055 (9)	0.0158 (11)	−0.0011 (9)
N2	0.0636 (15)	0.0432 (13)	0.0635 (17)	0.0047 (11)	0.0229 (14)	0.0007 (11)
N3	0.0418 (12)	0.0480 (14)	0.0724 (17)	0.0017 (11)	0.0154 (13)	−0.0003 (13)
O1	0.0638 (16)	0.0579 (14)	0.094 (2)	0.0036 (12)	−0.0086 (14)	0.0108 (13)
O2	0.0610 (14)	0.0595 (14)	0.0835 (17)	0.0097 (11)	−0.0034 (14)	−0.0153 (12)
O3	0.0633 (15)	0.0508 (13)	0.120 (2)	0.0005 (11)	0.0085 (16)	−0.0118 (13)
C1	0.0483 (17)	0.0421 (14)	0.0417 (17)	−0.0008 (12)	0.0183 (13)	−0.0006 (12)
C2	0.0452 (14)	0.0516 (16)	0.0454 (17)	−0.0025 (13)	0.0146 (14)	−0.0027 (13)
C3	0.0578 (17)	0.0450 (15)	0.058 (2)	−0.0104 (12)	0.0268 (16)	−0.0094 (12)
C4	0.063 (2)	0.0416 (15)	0.0499 (18)	0.0049 (13)	0.0278 (16)	0.0012 (13)
C5	0.0469 (16)	0.0508 (15)	0.0534 (19)	0.0053 (13)	0.0190 (14)	0.0059 (12)
C6	0.090 (3)	0.0451 (16)	0.098 (3)	0.0128 (16)	0.046 (2)	0.0119 (17)

Geometric parameters (Å, º) top

N1—C1	1.342 (4)	C2—C3	1.354 (4)
N1—C5	1.362 (4)	C2—H2	0.9300
N1—H1	0.8600	C3—C4	1.394 (4)
N2—C1	1.331 (4)	C3—H3	0.9300
N2—H2A	0.8600	C4—C5	1.351 (4)
N2—H2B	0.8600	C4—C6	1.516 (4)
N3—O3	1.223 (3)	C5—H5	0.9300
N3—O2	1.241 (3)	C6—H6A	0.9600
N3—O1	1.241 (3)	C6—H6B	0.9600
C1—C2	1.408 (4)	C6—H6C	0.9600

C1—N1—C5	123.2 (2)	C2—C3—C4	122.3 (3)
C1—N1—H1	118.4	C2—C3—H3	118.8
C5—N1—H1	118.4	C4—C3—H3	118.8
C1—N2—H2A	120.0	C5—C4—C3	116.7 (2)
C1—N2—H2B	120.0	C5—C4—C6	121.4 (3)
H2A—N2—H2B	120.0	C3—C4—C6	121.8 (3)
O3—N3—O2	120.3 (3)	C4—C5—N1	121.2 (3)
O3—N3—O1	120.3 (3)	C4—C5—H5	119.4
O2—N3—O1	119.4 (2)	N1—C5—H5	119.4
N2—C1—N1	119.9 (3)	C4—C6—H6A	109.5
N2—C1—C2	123.1 (3)	C4—C6—H6B	109.5
N1—C1—C2	116.9 (2)	H6A—C6—H6B	109.5
C3—C2—C1	119.6 (3)	C4—C6—H6C	109.5
C3—C2—H2	120.2	H6A—C6—H6C	109.5
C1—C2—H2	120.2	H6B—C6—H6C	109.5

C5—N1—C1—N2	−179.3 (3)	C2—C3—C4—C5	−1.0 (4)
C5—N1—C1—C2	0.4 (4)	C2—C3—C4—C6	179.9 (3)
N2—C1—C2—C3	179.5 (3)	C3—C4—C5—N1	1.1 (4)
N1—C1—C2—C3	−0.2 (4)	C6—C4—C5—N1	−179.8 (3)
C1—C2—C3—C4	0.6 (4)	C1—N1—C5—C4	−0.8 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.86	1.95	2.808 (4)	177
N1—H1···O3ⁱ	0.86	2.53	3.122 (4)	127
N2—H2A···O1	0.86	2.18	2.992 (4)	157
N2—H2B···O1ⁱⁱ	0.86	2.12	2.948 (4)	160
C2—H2···O3ⁱⁱ	0.93	2.45	3.304 (4)	153

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

Experimental details

Crystal data
Chemical formula	C₆H₉N₂⁺·NO₃⁻
M_r	171.16
Crystal system, space group	Monoclinic, Cc
Temperature (K)	298
a, b, c (Å)	8.7711 (7), 15.7261 (13), 6.8539 (5)
β (°)	117.455 (2)
V (Å³)	838.92 (12)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.49 × 0.38 × 0.21

Data collection
Diffractometer	Bruker SMART CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.948, 0.977
No. of measured, independent and observed [I > 2σ(I)] reflections	2040, 1251, 1077
R_int	0.031
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.109, 1.08
No. of reflections	1251
No. of parameters	111
No. of restraints	2
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.15, −0.13

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.86	1.95	2.808 (4)	177
N2—H2A···O1	0.86	2.18	2.992 (4)	157
N2—H2B···O1ⁱⁱ	0.86	2.12	2.948 (4)	160
C2—H2···O3ⁱⁱ	0.93	2.45	3.304 (4)	153

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

Acknowledgements

The research was supported by the National Natural Science Foundation of China (grant Nos. 20971115 and 21071134).

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