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Acta Crystallogr Sect E Struct Rep Online. 2010 March 1; 66(Pt 3): o662.
Published online 2010 February 20. doi:  10.1107/S1600536810005970
PMCID: PMC2983647

2-Amino-5-methyl­pyridinium nicotinate

Abstract

In the title compound, C6H9N2 +·C6H4NO2 , the 2-amino-5-methyl­pyridinium cation is essentially planar, with a maximum deviation of 0.023 (2) Å. In the crystal, the cations and anions are linked via strong N—H(...)O hydrogen bonds, forming a two dimensional network parallel to (100). In addition, π(...)π inter­actions involving the pyridinium and pyridine rings, with centroid–centroid distances of 3.6383 (8) Å, are observed.

Related literature

For background to the chemistry of substituted pyridines, see: Pozharski et al. (1997 [triangle]); Katritzky et al. (1996 [triangle]). For nicotinic acid, see: Athimoolam & Rajaram (2005 [triangle]); Lorenzen et al. (2001 [triangle]); Gielen et al. (1992 [triangle]); Kim et al. (2004 [triangle]). For a related structure, see: Nahringbauer & Kvick (1977 [triangle]). For details of hydrogen bonding, see: Jeffrey & Saenger (1991 [triangle]); Jeffrey (1997 [triangle]); Scheiner (1997 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o662-scheme1.jpg

Experimental

Crystal data

  • C6H9N2 +·C6H4NO2
  • M r = 231.25
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o662-efi1.jpg
  • a = 9.4877 (3) Å
  • b = 11.1403 (3) Å
  • c = 11.7611 (3) Å
  • β = 110.113 (2)°
  • V = 1167.29 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 296 K
  • 0.63 × 0.11 × 0.11 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.944, T max = 0.990
  • 14482 measured reflections
  • 3870 independent reflections
  • 2240 reflections with I > 2σ(I)
  • R int = 0.026

Refinement

  • R[F 2 > 2σ(F 2)] = 0.050
  • wR(F 2) = 0.144
  • S = 1.05
  • 3870 reflections
  • 195 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.20 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [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/S1600536810005970/sj2728sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810005970/sj2728Isup2.hkl

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

Acknowledgments

MH and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. MH thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

supplementary crystallographic information

Comment

Pyridine and its derivatives play important roles in heterocyclic chemistry (Pozharski et al., 1997; Katritzky et al., 1996). They are often involved in hydrogen-bond interactions (Jeffrey & Saenger, 1991; Jeffrey, 1997; Scheiner, 1997). Nicotinic acid (vitamin B3), known as niacin, is a lipid lowering agent widely used to treat hypertriglyceridemia by the inhibition of lipolysis in adipose tissue (Athimoolam & Rajaram, 2005). The nicotinic acid complex 5-methylpyrazine-2-carboxylic acid-4-oxide is a commonly used drug for the treatment of hypercholesterolemia (Lorenzen et al., 2001). Coordination complexes of nicotinic acid with metals such as Sn possess antitumour activity greater than the well known cisplatin or doxorubicin (Gielen et al., 1992). The enzyme nicotinic acid mononucleotide adenyltransferase is essential for the synthesis of nicotinamide adenine dinucleotide in all living cells and is a potential target for antibiotics (Kim et al., 2004). Since our aim is to study some interesting hydrogen bonding interactions, the crystal structure of the title compound is presented here.

The asymmetric unit (Fig. 1) contains one 2-amino-5-methylpyridinium cation and one nicotinate anion. The proton transfer from the carboxyl group to atom N1 of 2-amino-5-methylpyridine resulted in the widening of C1—N1—C5 angle of the pyridinium ring to 122.61 (11)°, compared to the corresponding angle of 117.4° in neutral 2-amino-5-methylpyridine (Nahringbauer & Kvick, 1977). The 2-amino-5-methylpyridinium cation is essentially planar, with a maximum deviation of 0.023 (2)Å for atom C6. The bond lengths are normal (Allen et al., 1987).

In the crystal packing (Fig. 2), the protonated N1 atom and the 2-amino group (N2) is hydrogen-bonded to the carboxylate oxygen atoms (O1 and O2) via a pair of intermolecular N1—H1N1···O2 and N2—H2N2···O1 hydrogen bonds forming an R22(8) ring motif (Bernstein et al., 1995). The intermolecular N2—H1N2···O2 hydrogen bonds connect these molecules into 2-dimensional networks parallel to the (100)-plane (see Table 1). The crystal structure is further stabilized by π···π interactions involving the pyridine (C7–C11/N3) and pyridinium (C1–C5/N1) rings, with centroid to centroid distance of 3.6383 (8)Å [symmetry code: 1-x, 1-y, 1-z].

Experimental

A hot methanol solution (20 ml) of 2-amino-5-methylpyridine (54 mg, Aldrich) and nicotinic acid (62 mg, Merck) were mixed and warmed over a heating magnetic stirrer for a few minutes. The resulting solution was allowed to cool slowly at room temperature and crystals of the title compound appeared after a few days.

Refinement

The methyl H atoms were positioned geometrically and were refined using a riding model, with Uiso(H) = 1.5Ueq(C). A rotating group model was used for the methyl group. The remaining H atoms were located in a difference map and refined freely [N–H = 0.883 (16)–0.988 (16)Å, C–H = 0.946 (13)–1.015 (17)Å].

Figures

Fig. 1.
The asymmetric unit of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.
The crystal packing of the title compound, showing hydrogen-bonded (dashed lines) networks.

Crystal data

C6H9N2+·C6H4NO2F(000) = 488
Mr = 231.25Dx = 1.316 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4062 reflections
a = 9.4877 (3) Åθ = 2.6–26.7°
b = 11.1403 (3) ŵ = 0.09 mm1
c = 11.7611 (3) ÅT = 296 K
β = 110.113 (2)°Needle, colourless
V = 1167.29 (6) Å30.63 × 0.11 × 0.11 mm
Z = 4

Data collection

Bruker SMART APEXII CCD area-detector diffractometer3870 independent reflections
Radiation source: fine-focus sealed tube2240 reflections with I > 2σ(I)
graphiteRint = 0.026
[var phi] and ω scansθmax = 31.6°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −13→13
Tmin = 0.944, Tmax = 0.990k = −15→16
14482 measured reflectionsl = −17→17

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)] = 0.050Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.144H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0668P)2 + 0.0299P] where P = (Fo2 + 2Fc2)/3
3870 reflections(Δ/σ)max < 0.001
195 parametersΔρmax = 0.20 e Å3
0 restraintsΔρmin = −0.20 e Å3

Special details

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.

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

xyzUiso*/Ueq
N10.02188 (12)0.19316 (10)0.05859 (9)0.0442 (3)
N2−0.10328 (14)0.22434 (12)0.19337 (12)0.0585 (3)
C1−0.00012 (14)0.16474 (11)0.16305 (10)0.0442 (3)
C20.08966 (14)0.07300 (12)0.23423 (12)0.0491 (3)
C30.19225 (14)0.01646 (12)0.19651 (12)0.0503 (3)
C40.21339 (13)0.04715 (12)0.08710 (11)0.0478 (3)
C50.12592 (14)0.13727 (12)0.02171 (11)0.0459 (3)
C60.33142 (17)−0.01226 (17)0.04856 (14)0.0688 (4)
H6A0.33130.0225−0.02620.103*
H6B0.3105−0.09660.03730.103*
H6C0.4280−0.00070.10980.103*
O10.72673 (12)0.39748 (10)1.02919 (8)0.0659 (3)
O20.86277 (12)0.36701 (9)0.91118 (8)0.0617 (3)
N30.68920 (14)0.67197 (11)0.70931 (11)0.0599 (3)
C70.58423 (16)0.73306 (14)0.73619 (15)0.0627 (4)
C80.53402 (17)0.70341 (14)0.82858 (16)0.0661 (4)
C90.59378 (16)0.60379 (13)0.89864 (14)0.0559 (4)
C100.70147 (13)0.53689 (11)0.87228 (11)0.0434 (3)
C110.74469 (15)0.57565 (12)0.77763 (12)0.0514 (3)
C120.76845 (14)0.42525 (11)0.94349 (11)0.0462 (3)
H2A0.0757 (14)0.0528 (11)0.3103 (13)0.053 (4)*
H3A0.2576 (15)−0.0480 (13)0.2476 (13)0.059 (4)*
H5A0.1359 (14)0.1651 (11)−0.0511 (12)0.047 (3)*
H7A0.5424 (18)0.8056 (15)0.6832 (15)0.076 (5)*
H8A0.458 (2)0.7512 (15)0.8436 (15)0.082 (5)*
H9A0.5651 (16)0.5825 (13)0.9650 (15)0.069 (5)*
H11A0.8211 (16)0.5323 (13)0.7567 (12)0.061 (4)*
H1N1−0.0397 (17)0.2561 (14)0.0051 (14)0.069 (4)*
H1N2−0.1231 (16)0.1988 (13)0.2573 (15)0.065 (4)*
H2N2−0.159 (2)0.2841 (16)0.1413 (16)0.081 (5)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0485 (5)0.0474 (6)0.0391 (5)0.0001 (5)0.0180 (4)0.0027 (5)
N20.0715 (8)0.0654 (8)0.0503 (6)0.0121 (6)0.0358 (6)0.0098 (6)
C10.0494 (6)0.0474 (7)0.0389 (6)−0.0066 (5)0.0191 (5)−0.0013 (5)
C20.0515 (7)0.0553 (8)0.0425 (6)−0.0048 (6)0.0186 (5)0.0082 (6)
C30.0462 (7)0.0532 (8)0.0502 (7)−0.0018 (6)0.0150 (6)0.0085 (6)
C40.0437 (6)0.0549 (8)0.0461 (7)−0.0036 (6)0.0171 (5)−0.0009 (6)
C50.0468 (7)0.0558 (8)0.0380 (6)−0.0039 (6)0.0183 (5)0.0002 (6)
C60.0611 (8)0.0880 (11)0.0618 (9)0.0186 (8)0.0268 (7)0.0076 (8)
O10.0818 (7)0.0743 (7)0.0557 (6)0.0160 (5)0.0417 (5)0.0135 (5)
O20.0788 (6)0.0671 (6)0.0499 (5)0.0249 (5)0.0358 (5)0.0115 (4)
N30.0668 (7)0.0543 (7)0.0576 (7)0.0011 (6)0.0199 (6)0.0071 (6)
C70.0590 (8)0.0479 (8)0.0726 (10)−0.0014 (7)0.0117 (7)0.0052 (7)
C80.0556 (8)0.0504 (8)0.0954 (12)0.0041 (7)0.0299 (8)−0.0050 (8)
C90.0571 (8)0.0506 (8)0.0680 (9)−0.0019 (6)0.0318 (7)−0.0043 (7)
C100.0427 (6)0.0455 (7)0.0425 (6)−0.0028 (5)0.0154 (5)−0.0048 (5)
C110.0545 (7)0.0530 (8)0.0495 (7)0.0018 (6)0.0214 (6)0.0005 (6)
C120.0519 (7)0.0514 (8)0.0376 (6)0.0001 (6)0.0185 (5)−0.0050 (5)

Geometric parameters (Å, °)

N1—C11.3526 (14)C6—H6B0.9600
N1—C51.3582 (16)C6—H6C0.9600
N1—H1N10.988 (16)O1—C121.2420 (14)
N2—C11.3289 (17)O2—C121.2650 (15)
N2—H1N20.883 (16)N3—C71.331 (2)
N2—H2N20.936 (19)N3—C111.3354 (17)
C1—C21.4073 (18)C7—C81.368 (2)
C2—C31.3558 (18)C7—H7A1.015 (17)
C2—H2A0.974 (14)C8—C91.382 (2)
C3—C41.4108 (18)C8—H8A0.964 (18)
C3—H3A1.002 (14)C9—C101.3832 (18)
C4—C51.3598 (18)C9—H9A0.941 (16)
C4—C61.4989 (19)C10—C111.3812 (17)
C5—H5A0.946 (13)C10—C121.5121 (18)
C6—H6A0.9600C11—H11A0.970 (15)
C1—N1—C5122.61 (11)H6A—C6—H6B109.5
C1—N1—H1N1120.1 (8)C4—C6—H6C109.5
C5—N1—H1N1117.3 (8)H6A—C6—H6C109.5
C1—N2—H1N2117.4 (10)H6B—C6—H6C109.5
C1—N2—H2N2119.0 (10)C7—N3—C11116.12 (13)
H1N2—N2—H2N2123.2 (14)N3—C7—C8123.94 (14)
N2—C1—N1118.99 (12)N3—C7—H7A115.3 (9)
N2—C1—C2123.65 (11)C8—C7—H7A120.7 (9)
N1—C1—C2117.35 (11)C7—C8—C9118.93 (14)
C3—C2—C1119.90 (12)C7—C8—H8A120.1 (10)
C3—C2—H2A122.2 (7)C9—C8—H8A120.9 (10)
C1—C2—H2A117.9 (7)C8—C9—C10118.82 (14)
C2—C3—C4121.95 (13)C8—C9—H9A121.4 (9)
C2—C3—H3A120.2 (8)C10—C9—H9A119.8 (9)
C4—C3—H3A117.9 (8)C11—C10—C9117.33 (13)
C5—C4—C3116.37 (12)C11—C10—C12121.26 (11)
C5—C4—C6121.94 (12)C9—C10—C12121.41 (12)
C3—C4—C6121.61 (12)N3—C11—C10124.84 (13)
N1—C5—C4121.81 (12)N3—C11—H11A114.9 (8)
N1—C5—H5A116.7 (8)C10—C11—H11A120.2 (8)
C4—C5—H5A121.5 (8)O1—C12—O2124.88 (12)
C4—C6—H6A109.5O1—C12—C10117.64 (11)
C4—C6—H6B109.5O2—C12—C10117.48 (10)
C5—N1—C1—N2179.41 (11)N3—C7—C8—C9−0.5 (2)
C5—N1—C1—C2−0.22 (18)C7—C8—C9—C10−0.5 (2)
N2—C1—C2—C3179.87 (12)C8—C9—C10—C111.1 (2)
N1—C1—C2—C3−0.52 (18)C8—C9—C10—C12−178.48 (12)
C1—C2—C3—C40.4 (2)C7—N3—C11—C10−0.3 (2)
C2—C3—C4—C50.46 (19)C9—C10—C11—N3−0.7 (2)
C2—C3—C4—C6177.42 (13)C12—C10—C11—N3178.87 (12)
C1—N1—C5—C41.14 (19)C11—C10—C12—O1178.34 (12)
C3—C4—C5—N1−1.21 (18)C9—C10—C12—O1−2.15 (19)
C6—C4—C5—N1−178.16 (12)C11—C10—C12—O2−1.73 (19)
C11—N3—C7—C80.9 (2)C9—C10—C12—O2177.79 (12)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N1···O2i0.988 (16)1.703 (16)2.6899 (15)176.8 (16)
N2—H1N2···O2ii0.883 (16)1.999 (16)2.8756 (17)171.7 (15)
N2—H2N2···O1i0.936 (18)1.878 (18)2.8122 (17)176.6 (17)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SJ2728).

References

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