2-Amino-5-bromo­pyridinium 4-carb­oxy­butano­ate

In the title salt, C₅H₆BrN₂⁺·C₅H₇O₄⁻, the 2-amino-5-bromo­pyridinium cation is essentially planar, with a maximum deviation of 0.005 (3) Å. In the crystal structure, the proton­ated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms of the anion via a pair of N—H...O hydrogen bonds, forming an R₂²(8) ring motif. The ion pairs are further connected via O—H...O, N—H...O and C—H...O hydrogen bonds, forming a two-dimensional network parallel to the bc plane. In the network, the hydrogen glutarate (4-carb­oxy­butano­ate) anions self-assemble through O—H...O hydrogen bonds, forming a supra­molecular chain along the c axis.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.041
• wR factor = 0.116
• Data-to-parameter ratio = 24.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C11
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.05
PLAT354_ALERT_3_C Short   O-H Bond (0.82A)   O4     -   H1O4   ...       0.69 Ang.
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          2
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          2
PLAT042_ALERT_1_C Calc. and Reported MoietyFormula Strings  Differ          ?
PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L=  0.600          7

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           31.82
           From the CIF: _reflns_number_total               4149
           Count of symmetry unique reflns         2425
           Completeness (_total/calc)            171.09%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      1724
           Fraction of Friedel pairs measured     0.711
           Are heavy atom types Z>Si present        yes
PLAT917_ALERT_2_G The FCF is likely NOT based on a BASF/TWIN Flack          !
PLAT063_ALERT_4_G Crystal Size Likely too Large for Beam Size ....       0.72 mm
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          4

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   7 ALERT level C = Check and explain
   4 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   3 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   4 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Weak interactions, such as hydrogen bonding and π–π stacking, have attracted much interest as a result of their significance in chemistry and biology, especially in the field of crystal engineering (Moghimi et al., 2002; Aghabozorg et al., 2005). The design of highly specific solid-state compounds is of considerable significance in organic chemistry due to the important applications of these compounds in the development of new optical, magnetic and electronic systems (Lehn, 1992). The present work is part of a structural study of complexes of 2-amino pyridinium systems with hydrogen-bond donors and we report here the structure of 2-amino-5-bromopyridinium hydrogen glutarate, (I).

The asymmetric unit (Fig. 1) contains a 2-amino-5-bromopyridinium cation and a hydrogen glutarate anion. The 2-amino-5-bromopyridinium cation is essentially planar, with a maximum deviation of 0.005 (3) Å for atom C5. In the 2-amino-5-bromopyridinium cation, a wider than normal angle [C6—N1—C2 = 123.8 (2)°] is subtented at the protonated N1 atom. The backbone conformation of the hydrogen glutarate anion can be described by the two torsion angles C8-C9-C10-C11 of -178.0 (2)° and C7-C8-C9-C10 of -71.7 (3)°. As evident from the torsion angles, the backbone is in a fully extended conformation (Saraswathi et al., 2001) of the two carboxyl groups, one is deprotonated while the other is not. The bond lengths (Allen et al., 1987) and angles are within normal ranges.

In the crystal packing, 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–H1N2···O1 hydrogen bonds forming a ring motif R₂²(8) (Bernstein et al., 1995). The ion pairs are further connected via N2—H2N2···O1, O4—H1O4···O2 and C6—H6A···O3 (Table 1) hydrogen bonds, forming a two-dimensional network parallel to the bc-plane (Fig. 2). The hydrogen glutarate anions self-assemble through O4—H1O4···O2 hydrogen bonds, forming one-dimensional supramolecular chains along the c-axis (Fig. 3). Furthermore, the ion pairs are stacked down along the a-axis, forming a three-dimensional network as shown in Fig. 4.

Related literature

For applications of weak interactions, see: Moghimi et al. (2002); Aghabozorg et al. (2005); Lehn (1992). For the conformation of glutaric acid, see: Saraswathi et al. (2001). For hydrogen-bond motifs, see: Bernstein et al. (1995). For bond-length data, see: Allen et al. (1987).

S2. Experimental

A hot methanol solution (20 ml) of 2-amino-5-bromopyridine (86 mg, Aldrich) and glutaric acid (66 mg, Merck) were mixed and warmed over a heating magnetic stirrer hotplate 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.

S3. Refinement

Atoms H1N1, H1N2, H2N2 and H1O4 were located from a difference Fourier map and were refined freely [N—H= 0.83 (4)–0.94 (3) Å and O—H = 0.69 (5) Å]. The remaining hydrogen atoms were positioned geometrically [C—H = 0.93 or 0.97 Å] and were refined using a riding model, with U_iso(H) = 1.2U_eq(C). 1734 Friedel pairs were used to determine the absolute configuration.

Computing details

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); 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) and PLATON (Spek, 2009).

Figures

	Fig. 1. The asymmetric unit of the title compound. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. The crystal packing of (I), showing hydrogen-bonded (dashed lines) 2D networks parallel to to the bc-plane. H atoms not involved in the intermolecular interactions have been omitted for clarity.
	Fig. 3. Carboxyl-carboxylate interactions made up of hydrogen glutarate anion.
	Fig. 4. The crystal packing of the title compound (I), showing the stacking of the molecules down the a-axis. H atoms not involved in the intermolecular interactions have been omitted for clarity.

2-amino-5-bromopyridinium 4-carboxybutanoate

Crystal data

C5H6BrN2^+·C5H7O4^−	F(000) = 616
Mr = 305.13	Dx = 1.653 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 2942 reflections
a = 5.1499 (12) Å	θ = 2.7–26.8°
b = 14.858 (4) Å	µ = 3.36 mm^−1
c = 16.022 (4) Å	T = 296 K
V = 1226.0 (5) Å^3	Block, colourless
Z = 4	0.72 × 0.31 × 0.15 mm

Data collection

Bruker APEXII DUO CCD area-detector diffractometer	4149 independent reflections
Radiation source: fine-focus sealed tube	2911 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.035
φ and ω scans	θmax = 31.8°, θmin = 2.7°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −7→7
Tmin = 0.195, Tmax = 0.628	k = −22→21
8937 measured reflections	l = −21→23

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.041	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.116	w = 1/[σ^2(Fo^2) + (0.0414P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 1.02	(Δ/σ)max = 0.001
4149 reflections	Δρmax = 0.59 e Å^−3
170 parameters	Δρmin = −0.42 e Å^−3
0 restraints	Absolute structure: Flack (1983), 1734 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.024 (9)

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 (Ų)

	x	y	z	Uiso*/Ueq
Br1	0.34848 (8)	0.78522 (2)	0.59104 (2)	0.06364 (14)
N1	−0.1456 (5)	0.72632 (14)	0.78238 (14)	0.0388 (5)
N2	−0.2377 (6)	0.7831 (2)	0.91338 (17)	0.0548 (6)
C6	−0.0182 (6)	0.72501 (17)	0.70949 (16)	0.0400 (6)
H6A	−0.0563	0.6812	0.6699	0.048*
C5	0.1666 (6)	0.78770 (17)	0.69349 (17)	0.0424 (5)
C4	0.2211 (6)	0.8540 (2)	0.7532 (2)	0.0508 (7)
H4A	0.3458	0.8977	0.7425	0.061*
C3	0.0906 (6)	0.8540 (2)	0.8269 (2)	0.0506 (7)
H3A	0.1271	0.8977	0.8668	0.061*
C2	−0.1011 (6)	0.78778 (19)	0.84360 (16)	0.0412 (6)
O1	0.3976 (5)	0.64368 (15)	0.92821 (11)	0.0543 (6)
O2	0.5093 (4)	0.59455 (14)	0.80384 (11)	0.0464 (5)
O3	−0.1981 (4)	0.44309 (18)	1.10571 (14)	0.0577 (6)
O4	0.1873 (5)	0.46064 (19)	1.16336 (14)	0.0582 (6)
C7	0.3666 (5)	0.59209 (17)	0.86815 (13)	0.0345 (5)
C8	0.1501 (6)	0.52312 (18)	0.86922 (15)	0.0402 (5)
H8A	0.2232	0.4648	0.8554	0.048*
H8B	0.0267	0.5384	0.8257	0.048*
C9	0.0036 (6)	0.5146 (2)	0.95136 (17)	0.0405 (6)
H9A	−0.0472	0.5740	0.9706	0.049*
H9B	−0.1529	0.4795	0.9427	0.049*
C10	0.1701 (6)	0.46966 (19)	1.01720 (16)	0.0426 (6)
H10A	0.2264	0.4115	0.9965	0.051*
H10B	0.3239	0.5060	1.0266	0.051*
C11	0.0308 (5)	0.45656 (16)	1.09925 (16)	0.0369 (5)
H1N1	−0.270 (6)	0.681 (2)	0.7886 (19)	0.037 (7)*
H1N2	−0.335 (8)	0.740 (3)	0.923 (2)	0.045 (9)*
H2N2	−0.188 (8)	0.813 (2)	0.954 (2)	0.054 (10)*
H1O4	0.132 (11)	0.454 (3)	1.202 (3)	0.077 (15)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Br1	0.0722 (2)	0.05631 (18)	0.0624 (2)	−0.00719 (18)	0.02248 (18)	0.00228 (16)
N1	0.0394 (12)	0.0371 (10)	0.0400 (11)	−0.0100 (11)	−0.0015 (9)	−0.0063 (8)
N2	0.0634 (16)	0.0631 (15)	0.0380 (12)	−0.0189 (14)	−0.0009 (11)	−0.0141 (14)
C6	0.0444 (15)	0.0366 (12)	0.0390 (12)	−0.0025 (12)	−0.0050 (11)	−0.0050 (10)
C5	0.0438 (14)	0.0356 (11)	0.0479 (13)	−0.0004 (14)	0.0004 (12)	0.0015 (11)
C4	0.0439 (16)	0.0413 (14)	0.067 (2)	−0.0096 (13)	0.0036 (14)	−0.0033 (13)
C3	0.0520 (18)	0.0437 (13)	0.0562 (17)	−0.0128 (14)	−0.0056 (14)	−0.0111 (13)
C2	0.0463 (15)	0.0392 (12)	0.0380 (12)	−0.0033 (12)	−0.0070 (11)	−0.0055 (11)
O1	0.0721 (16)	0.0581 (11)	0.0327 (9)	−0.0205 (12)	0.0154 (9)	−0.0153 (8)
O2	0.0526 (12)	0.0619 (11)	0.0247 (8)	−0.0177 (11)	0.0048 (8)	−0.0074 (8)
O3	0.0367 (11)	0.0894 (16)	0.0470 (12)	−0.0027 (11)	0.0051 (9)	0.0139 (11)
O4	0.0492 (13)	0.0935 (18)	0.0320 (10)	−0.0119 (13)	0.0026 (10)	0.0173 (11)
C7	0.0397 (13)	0.0409 (12)	0.0229 (10)	−0.0022 (12)	−0.0023 (10)	0.0006 (8)
C8	0.0458 (14)	0.0450 (13)	0.0299 (11)	−0.0065 (13)	−0.0016 (11)	0.0015 (10)
C9	0.0369 (14)	0.0496 (13)	0.0349 (12)	−0.0016 (12)	0.0020 (11)	0.0095 (11)
C10	0.0399 (14)	0.0534 (14)	0.0344 (12)	0.0064 (14)	0.0079 (11)	0.0096 (10)
C11	0.0432 (14)	0.0351 (11)	0.0324 (12)	0.0038 (10)	0.0077 (11)	0.0064 (10)

Geometric parameters (Å, º)

Br1—C5	1.890 (3)	O2—C7	1.266 (3)
N1—C6	1.340 (4)	O3—C11	1.201 (4)
N1—C2	1.360 (3)	O4—C11	1.307 (4)
N1—H1N1	0.94 (3)	O4—H1O4	0.69 (5)
N2—C2	1.323 (4)	C7—C8	1.514 (4)
N2—H1N2	0.83 (4)	C8—C9	1.522 (4)
N2—H2N2	0.83 (4)	C8—H8A	0.9700
C6—C5	1.356 (4)	C8—H8B	0.9700
C6—H6A	0.9300	C9—C10	1.515 (4)
C5—C4	1.402 (4)	C9—H9A	0.9700
C4—C3	1.359 (5)	C9—H9B	0.9700
C4—H4A	0.9300	C10—C11	1.510 (4)
C3—C2	1.419 (4)	C10—H10A	0.9700
C3—H3A	0.9300	C10—H10B	0.9700
O1—C7	1.241 (3)
C6—N1—C2	123.8 (2)	O1—C7—C8	120.3 (2)
C6—N1—H1N1	114.6 (19)	O2—C7—C8	117.1 (2)
C2—N1—H1N1	121.7 (19)	C7—C8—C9	115.5 (2)
C2—N2—H1N2	122 (2)	C7—C8—H8A	108.4
C2—N2—H2N2	119 (3)	C9—C8—H8A	108.4
H1N2—N2—H2N2	116 (4)	C7—C8—H8B	108.4
N1—C6—C5	119.9 (2)	C9—C8—H8B	108.4
N1—C6—H6A	120.0	H8A—C8—H8B	107.5
C5—C6—H6A	120.0	C10—C9—C8	111.0 (2)
C6—C5—C4	119.6 (3)	C10—C9—H9A	109.4
C6—C5—Br1	119.9 (2)	C8—C9—H9A	109.4
C4—C5—Br1	120.5 (2)	C10—C9—H9B	109.4
C3—C4—C5	119.6 (3)	C8—C9—H9B	109.4
C3—C4—H4A	120.2	H9A—C9—H9B	108.0
C5—C4—H4A	120.2	C11—C10—C9	113.2 (2)
C4—C3—C2	120.5 (3)	C11—C10—H10A	108.9
C4—C3—H3A	119.7	C9—C10—H10A	108.9
C2—C3—H3A	119.7	C11—C10—H10B	108.9
N2—C2—N1	119.0 (3)	C9—C10—H10B	108.9
N2—C2—C3	124.4 (3)	H10A—C10—H10B	107.7
N1—C2—C3	116.6 (3)	O3—C11—O4	123.1 (3)
C11—O4—H1O4	117 (5)	O3—C11—C10	124.3 (3)
O1—C7—O2	122.6 (3)	O4—C11—C10	112.7 (2)
C2—N1—C6—C5	−0.2 (4)	C4—C3—C2—N2	−179.7 (3)
N1—C6—C5—C4	−0.6 (4)	C4—C3—C2—N1	−0.4 (4)
N1—C6—C5—Br1	179.5 (2)	O1—C7—C8—C9	−7.5 (4)
C6—C5—C4—C3	0.8 (5)	O2—C7—C8—C9	173.0 (2)
Br1—C5—C4—C3	−179.2 (3)	C7—C8—C9—C10	−71.7 (3)
C5—C4—C3—C2	−0.3 (5)	C8—C9—C10—C11	−178.0 (2)
C6—N1—C2—N2	−179.9 (3)	C9—C10—C11—O3	32.0 (4)
C6—N1—C2—C3	0.7 (4)	C9—C10—C11—O4	−148.6 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N1···O2^i	0.94 (3)	1.73 (3)	2.666 (3)	177 (2)
N2—H1N2···O1^i	0.83 (4)	1.99 (4)	2.806 (4)	170 (4)
N2—H2N2···O1^ii	0.83 (3)	2.04 (3)	2.848 (3)	164 (3)
O4—H1O4···O2^iii	0.69 (5)	1.93 (5)	2.601 (3)	166 (5)
C3—H3A···O3^iv	0.93	2.57	3.382 (4)	146
C6—H6A···O3^v	0.93	2.46	3.337 (4)	157

Symmetry codes: (i) x−1, y, z; (ii) x−1/2, −y+3/2, −z+2; (iii) −x+1/2, −y+1, z+1/2; (iv) x+1/2, −y+3/2, −z+2; (v) −x−1/2, −y+1, z−1/2.