organic compounds
Bis(2-amino-5-bromopyridinium) fumarate dihydrate
aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my
In the title compound, 2C5H6BrN2+·C4H2O42−·2H2O, the complete fumarate dianion is generated by crystallographic inversion symmetry. The cation is approximately planar, with a maximum deviation of 0.036 (1) Å. In the anion, the carboxylate group is twisted slightly away from the attached plane; the dihedral angle between carboxylate and (E)-but-2-ene planes is 6.11 (14)°. In the crystal, the carboxylate O atoms form bifurcated (N—H⋯O and C—H⋯O) and N—H⋯O hydrogen bonds with the cations. The crystal packing is stabilized by R22(8) ring motifs which are generated by pairs of N—H⋯O hydrogen bonds. The is further consolidated by water molecules via O(water)—H⋯O and N—H⋯O(water) hydrogen bonds. The components are linked by these interactions into three-dimensional network.
Related literature
For details of hydrogen bonding, see: Goswami & Ghosh (1997); Goswami et al. (1998). For applications of fumaric acid, see: Batchelor et al. (2000). For related structures, see: Büyükgüngör et al. (2004); Büyükgüngör & Odabąsoğlu (20065); Hemamalini & Fun, (2010a,b); Quah et al. (2008; 2010a,b). For bond-length data, see: Allen et al. (1987). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986). For hydrogen-bond motifs, see: Bernstein et al. (1995).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
https://doi.org/10.1107/S1600536810030989/bt5312sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810030989/bt5312Isup2.hkl
A hot methanol solution (20 ml) of 2-amino-5-bromopyridine (86 mg, Aldrich) and fumaric acid (58 mg, Merck) was mixed and warmed over a 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.
O– and N– bound H atoms were located in a difference Fourier map and allowed to refined freely. The rest of the hydrogen atoms were positioned geometrically and refined using a riding model with C—H = 0.93 Å and Uiso(H) = 1.2 Ueq(C). The highest residual electron density peak is located at 0.66 Å from C6 and the deepest hole is located at 1.19 Å from Br1.
Hydrogen bonding plays a key role in molecular recognition (Goswami & Ghosh, 1997) and crystal engineering research (Goswami et al., 1998). Fumaric acid, the E isomer of butenedioic acid, is of interest since it is known to form supramolecular assemblies with N-aromatic compounds (Batchelor et al., 2000). It tends to form infinite chains arranged in a nearly coplanar manner via pairs of strong O—H···O hydrogen bonds. The crystal structures of 2-aminopyridinium-fumarate-fumaric acid (2/1/1) (Büyükgüngör et al., 2004) and 2,6-diamino pyridinium hydrogen fumarate (Büyükgüngör & Odabąsoǧlu, 2006) have been reported in the literature. We have recently reported the crystal structures of 2-amino-5-chloropyridine-fumaric acid (1/2) (Hemamalini & Fun, 2010a) and 2-amino-4-methylpyridinium (E)-3-carboxyprop-2-enoate (Hemamalini & Fun, 2010b) from our laboratory. In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title compound, (I), is presented here.
The
of title compound (Fig. 1), consist of a protonated 2-amino-5-bromopyridinium cation, a half molecule of fumarate anion and a water molecule. The fumarate anion is lying about an inversion center (symmetry code: -x + 1, -y + 1, -z). In the 2-amino-5-bromopyridinium cation, protonatation of N1 atom has lead to a slight increase in the C1–N1–C5 angle to 122.64 (11)°. The 2-amino-5-bromopyridinium cation is approximately planar, with a maximum deviation of 0.036 (1) Å for atom N2. In fumarate anion, C6/C7/C6A/C7A plane is planar with an r.m.s deviation of <0.001 (1) Å. This plane makes a dihedral angle of 6.90 (6)° with 2-amino-5-bromopyridinium cation. In the anion, the carboxylate group is twisted slightly away from the attached plane; the dihedral angle between C6/C7/C6A/C7A and O1/O2/C6/C7 planes is 6.11 (14)°.In the crystal packing (Fig. 2), the carboxylate oxygen atoms, O2 and O3 form bifurcated (N2–H1N2···O2 and C3–H3A···O2) and N1–H1N1···O1 hydrogen bonds, respectively, with cations. The crystal packing is stabilized by R22(8) ring motifs (Bernstein et al., 1995) which are generated by pairs of N–H···O hydrogen bonds (Table 1). The
is further consolidated by water molecules via O1W–H1W1···O1, O1W–H2W1···O1 and N2–H2N2···O1W hydrogen bonds. The anions, cations and water molecules are linked by these interactions into three-dimensional network.For details of hydrogen bonding, see: Goswami & Ghosh (1997); Goswami et al. (1998). For applications of fumaric acid, see: Batchelor et al. (2000). For related structures, see: Büyükgüngör et al. (2004); Büyükgüngör & Odabąsoǧlu (20065); Hemamalini & Fun, (2010a,b); Quah et al. (2008; 2010a,b). For bond-length data, see: Allen et al. (1987). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986). For hydrogen-bond motifs, see: Bernstein et al. (1995).
Data collection: APEX2 (Bruker, 2009); cell
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).Fig. 1. The molecular structure of the title compound showing 50% probability displacement ellipsoids for non-H atoms and the atom-numbering scheme. Symmetry code: ($) -x + 1, -y + 1, -z. Intramolecular interactions are shown as dashed lines. | |
Fig. 2. The crystal structure of the title compound viewed along the a axis. H atoms not involved in intermolecular interactions (dashed lines) have been omitted for clarity. |
2C5H6BrN2+·C4H2O42−·2H2O | F(000) = 496 |
Mr = 498.14 | Dx = 1.856 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5779 reflections |
a = 8.3717 (1) Å | θ = 2.6–34.6° |
b = 16.5354 (2) Å | µ = 4.59 mm−1 |
c = 6.7846 (1) Å | T = 100 K |
β = 108.336 (1)° | Block, colourless |
V = 891.50 (2) Å3 | 0.39 × 0.15 × 0.12 mm |
Z = 2 |
Bruker SMART APEXII CCD area-detector diffractometer | 3942 independent reflections |
Radiation source: fine-focus sealed tube | 3252 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.028 |
φ and ω scans | θmax = 35.2°, θmin = 2.5° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −13→12 |
Tmin = 0.271, Tmax = 0.618 | k = −26→23 |
15040 measured reflections | l = −10→10 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.026 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.059 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0265P)2 + 0.2048P] where P = (Fo2 + 2Fc2)/3 |
3942 reflections | (Δ/σ)max = 0.001 |
138 parameters | Δρmax = 0.54 e Å−3 |
0 restraints | Δρmin = −0.39 e Å−3 |
2C5H6BrN2+·C4H2O42−·2H2O | V = 891.50 (2) Å3 |
Mr = 498.14 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.3717 (1) Å | µ = 4.59 mm−1 |
b = 16.5354 (2) Å | T = 100 K |
c = 6.7846 (1) Å | 0.39 × 0.15 × 0.12 mm |
β = 108.336 (1)° |
Bruker SMART APEXII CCD area-detector diffractometer | 3942 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 3252 reflections with I > 2σ(I) |
Tmin = 0.271, Tmax = 0.618 | Rint = 0.028 |
15040 measured reflections |
R[F2 > 2σ(F2)] = 0.026 | 0 restraints |
wR(F2) = 0.059 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.54 e Å−3 |
3942 reflections | Δρmin = −0.39 e Å−3 |
138 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. |
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. |
x | y | z | Uiso*/Ueq | ||
Br1 | 0.741696 (15) | 1.042853 (7) | 0.08809 (2) | 0.01677 (4) | |
N1 | 0.78272 (13) | 0.79718 (7) | 0.17705 (16) | 0.01325 (19) | |
H1N1 | 0.712 (2) | 0.7551 (11) | 0.133 (3) | 0.022 (4)* | |
N2 | 0.99471 (14) | 0.70859 (7) | 0.34946 (18) | 0.0152 (2) | |
H2N2 | 1.091 (3) | 0.7028 (12) | 0.426 (3) | 0.031 (5)* | |
H1N2 | 0.926 (2) | 0.6673 (12) | 0.296 (3) | 0.036 (5)* | |
C1 | 0.72188 (15) | 0.87250 (8) | 0.11482 (19) | 0.0142 (2) | |
H1A | 0.6112 | 0.8790 | 0.0301 | 0.017* | |
C2 | 0.82285 (16) | 0.93842 (8) | 0.1764 (2) | 0.0139 (2) | |
C3 | 0.99045 (15) | 0.92827 (8) | 0.3065 (2) | 0.0148 (2) | |
H3A | 1.0606 | 0.9729 | 0.3486 | 0.018* | |
C4 | 1.04836 (15) | 0.85246 (8) | 0.36957 (19) | 0.0144 (2) | |
H4A | 1.1575 | 0.8455 | 0.4585 | 0.017* | |
C5 | 0.94285 (15) | 0.78397 (8) | 0.30010 (18) | 0.0127 (2) | |
O1W | 0.34331 (12) | 0.71054 (7) | 0.61811 (17) | 0.0206 (2) | |
H2W1 | 0.392 (3) | 0.6972 (13) | 0.729 (3) | 0.038 (6)* | |
H1W1 | 0.396 (3) | 0.7487 (15) | 0.594 (4) | 0.043 (6)* | |
O1 | 0.55652 (11) | 0.67725 (5) | 0.02333 (15) | 0.01630 (18) | |
O2 | 0.75988 (11) | 0.58655 (6) | 0.15601 (16) | 0.01766 (18) | |
C6 | 0.48381 (16) | 0.53893 (7) | −0.0202 (2) | 0.0139 (2) | |
H6AA | 0.3763 | 0.5537 | −0.1026 | 0.017* | |
C7 | 0.61164 (15) | 0.60438 (7) | 0.06033 (19) | 0.0127 (2) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Br1 | 0.01516 (6) | 0.01024 (6) | 0.02259 (7) | 0.00028 (4) | 0.00262 (4) | 0.00195 (5) |
N1 | 0.0112 (4) | 0.0107 (5) | 0.0165 (5) | −0.0015 (4) | 0.0023 (4) | −0.0004 (4) |
N2 | 0.0124 (5) | 0.0108 (5) | 0.0201 (5) | −0.0002 (4) | 0.0017 (4) | 0.0006 (4) |
C1 | 0.0128 (5) | 0.0124 (5) | 0.0161 (5) | 0.0000 (4) | 0.0027 (4) | 0.0010 (4) |
C2 | 0.0137 (5) | 0.0103 (5) | 0.0170 (5) | 0.0005 (4) | 0.0040 (4) | 0.0008 (4) |
C3 | 0.0129 (5) | 0.0123 (5) | 0.0182 (6) | −0.0025 (4) | 0.0035 (4) | −0.0017 (4) |
C4 | 0.0117 (5) | 0.0129 (6) | 0.0162 (5) | −0.0016 (4) | 0.0011 (4) | −0.0019 (4) |
C5 | 0.0111 (5) | 0.0128 (5) | 0.0139 (5) | −0.0003 (4) | 0.0036 (4) | −0.0005 (4) |
O1W | 0.0163 (5) | 0.0189 (5) | 0.0221 (5) | −0.0039 (4) | −0.0003 (4) | 0.0050 (4) |
O1 | 0.0134 (4) | 0.0097 (4) | 0.0228 (5) | 0.0004 (3) | 0.0014 (3) | −0.0001 (3) |
O2 | 0.0120 (4) | 0.0126 (4) | 0.0245 (5) | 0.0001 (3) | 0.0002 (3) | −0.0001 (4) |
C6 | 0.0112 (5) | 0.0111 (5) | 0.0176 (5) | −0.0005 (4) | 0.0016 (4) | −0.0011 (4) |
C7 | 0.0130 (5) | 0.0105 (5) | 0.0138 (5) | −0.0010 (4) | 0.0030 (4) | −0.0001 (4) |
Br1—C2 | 1.8832 (13) | C3—H3A | 0.9300 |
N1—C5 | 1.3556 (15) | C4—C5 | 1.4223 (17) |
N1—C1 | 1.3616 (16) | C4—H4A | 0.9300 |
N1—H1N1 | 0.899 (18) | O1W—H2W1 | 0.77 (2) |
N2—C5 | 1.3278 (16) | O1W—H1W1 | 0.81 (2) |
N2—H2N2 | 0.81 (2) | O1—C7 | 1.2863 (15) |
N2—H1N2 | 0.89 (2) | O2—C7 | 1.2416 (14) |
C1—C2 | 1.3620 (17) | C6—C6i | 1.326 (2) |
C1—H1A | 0.9300 | C6—C7 | 1.4990 (17) |
C2—C3 | 1.4130 (17) | C6—H6AA | 0.9300 |
C3—C4 | 1.3635 (18) | ||
C5—N1—C1 | 122.64 (11) | C2—C3—H3A | 120.3 |
C5—N1—H1N1 | 119.8 (11) | C3—C4—C5 | 120.37 (11) |
C1—N1—H1N1 | 117.5 (12) | C3—C4—H4A | 119.8 |
C5—N2—H2N2 | 116.7 (14) | C5—C4—H4A | 119.8 |
C5—N2—H1N2 | 119.8 (13) | N2—C5—N1 | 119.22 (11) |
H2N2—N2—H1N2 | 123.4 (19) | N2—C5—C4 | 122.97 (11) |
N1—C1—C2 | 120.10 (11) | N1—C5—C4 | 117.81 (11) |
N1—C1—H1A | 119.9 | H2W1—O1W—H1W1 | 105 (2) |
C2—C1—H1A | 120.0 | C6i—C6—C7 | 123.34 (14) |
C1—C2—C3 | 119.67 (12) | C6i—C6—H6AA | 118.3 |
C1—C2—Br1 | 120.62 (9) | C7—C6—H6AA | 118.3 |
C3—C2—Br1 | 119.71 (9) | O2—C7—O1 | 124.24 (11) |
C4—C3—C2 | 119.37 (11) | O2—C7—C6 | 120.03 (11) |
C4—C3—H3A | 120.3 | O1—C7—C6 | 115.72 (11) |
C5—N1—C1—C2 | −0.12 (18) | C1—N1—C5—N2 | −178.04 (12) |
N1—C1—C2—C3 | −0.51 (19) | C1—N1—C5—C4 | 1.59 (17) |
N1—C1—C2—Br1 | 178.98 (9) | C3—C4—C5—N2 | 177.11 (13) |
C1—C2—C3—C4 | −0.42 (19) | C3—C4—C5—N1 | −2.50 (18) |
Br1—C2—C3—C4 | −179.92 (10) | C6i—C6—C7—O2 | 6.0 (2) |
C2—C3—C4—C5 | 1.93 (19) | C6i—C6—C7—O1 | −173.89 (16) |
Symmetry code: (i) −x+1, −y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O1 | 0.902 (18) | 1.815 (18) | 2.7136 (14) | 174.1 (19) |
N2—H2N2···O1Wii | 0.82 (2) | 2.11 (2) | 2.9143 (16) | 169.7 (19) |
N2—H1N2···O2 | 0.893 (19) | 1.946 (19) | 2.8348 (15) | 173.2 (19) |
O1W—H2W1···O1iii | 0.77 (2) | 2.07 (2) | 2.8213 (15) | 169 (2) |
O1W—H1W1···O1iv | 0.82 (3) | 1.99 (3) | 2.7865 (14) | 167 (3) |
C3—H3A···O2v | 0.93 | 2.41 | 3.3089 (17) | 162 |
Symmetry codes: (ii) x+1, y, z; (iii) x, y, z+1; (iv) x, −y+3/2, z+1/2; (v) −x+2, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | 2C5H6BrN2+·C4H2O42−·2H2O |
Mr | 498.14 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 8.3717 (1), 16.5354 (2), 6.7846 (1) |
β (°) | 108.336 (1) |
V (Å3) | 891.50 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 4.59 |
Crystal size (mm) | 0.39 × 0.15 × 0.12 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.271, 0.618 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 15040, 3942, 3252 |
Rint | 0.028 |
(sin θ/λ)max (Å−1) | 0.811 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.026, 0.059, 1.03 |
No. of reflections | 3942 |
No. of parameters | 138 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.54, −0.39 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N1···O1 | 0.902 (18) | 1.815 (18) | 2.7136 (14) | 174.1 (19) |
N2—H2N2···O1Wi | 0.82 (2) | 2.11 (2) | 2.9143 (16) | 169.7 (19) |
N2—H1N2···O2 | 0.893 (19) | 1.946 (19) | 2.8348 (15) | 173.2 (19) |
O1W—H2W1···O1ii | 0.77 (2) | 2.07 (2) | 2.8213 (15) | 169 (2) |
O1W—H1W1···O1iii | 0.82 (3) | 1.99 (3) | 2.7865 (14) | 167 (3) |
C3—H3A···O2iv | 0.9300 | 2.4100 | 3.3089 (17) | 162.00 |
Symmetry codes: (i) x+1, y, z; (ii) x, y, z+1; (iii) x, −y+3/2, z+1/2; (iv) −x+2, y+1/2, −z+1/2. |
Acknowledgements
The authors thank Universiti Sains Malaysia (USM) for the Research University Golden Goose Grant (1001/PFIZIK/811012). CKQ also thanks USM for the award of a USM fellowship and HM also thanks USM for the award of a postdoctoral fellowship.
References
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Hydrogen bonding plays a key role in molecular recognition (Goswami & Ghosh, 1997) and crystal engineering research (Goswami et al., 1998). Fumaric acid, the E isomer of butenedioic acid, is of interest since it is known to form supramolecular assemblies with N-aromatic compounds (Batchelor et al., 2000). It tends to form infinite chains arranged in a nearly coplanar manner via pairs of strong O—H···O hydrogen bonds. The crystal structures of 2-aminopyridinium-fumarate-fumaric acid (2/1/1) (Büyükgüngör et al., 2004) and 2,6-diamino pyridinium hydrogen fumarate (Büyükgüngör & Odabąsoǧlu, 2006) have been reported in the literature. We have recently reported the crystal structures of 2-amino-5-chloropyridine-fumaric acid (1/2) (Hemamalini & Fun, 2010a) and 2-amino-4-methylpyridinium (E)-3-carboxyprop-2-enoate (Hemamalini & Fun, 2010b) from our laboratory. In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title compound, (I), is presented here.
The asymmetric unit of title compound (Fig. 1), consist of a protonated 2-amino-5-bromopyridinium cation, a half molecule of fumarate anion and a water molecule. The fumarate anion is lying about an inversion center (symmetry code: -x + 1, -y + 1, -z). In the 2-amino-5-bromopyridinium cation, protonatation of N1 atom has lead to a slight increase in the C1–N1–C5 angle to 122.64 (11)°. The 2-amino-5-bromopyridinium cation is approximately planar, with a maximum deviation of 0.036 (1) Å for atom N2. In fumarate anion, C6/C7/C6A/C7A plane is planar with an r.m.s deviation of <0.001 (1) Å. This plane makes a dihedral angle of 6.90 (6)° with 2-amino-5-bromopyridinium cation. In the anion, the carboxylate group is twisted slightly away from the attached plane; the dihedral angle between C6/C7/C6A/C7A and O1/O2/C6/C7 planes is 6.11 (14)°.
In the crystal packing (Fig. 2), the carboxylate oxygen atoms, O2 and O3 form bifurcated (N2–H1N2···O2 and C3–H3A···O2) and N1–H1N1···O1 hydrogen bonds, respectively, with cations. The crystal packing is stabilized by R22(8) ring motifs (Bernstein et al., 1995) which are generated by pairs of N–H···O hydrogen bonds (Table 1). The crystal structure is further consolidated by water molecules via O1W–H1W1···O1, O1W–H2W1···O1 and N2–H2N2···O1W hydrogen bonds. The anions, cations and water molecules are linked by these interactions into three-dimensional network.