N,N′-Bis(5-bromo­pyridin-2-yl)methane­di­amine

The V-shaped title compound, C₁₁H₁₀Br₂N₄, lies on a crystallographic twofold rotation axis which passes through the central C atom. In the crystal, an infinite tape motif, which propagates in the a-axis direction, is formed by inversion-related N—H⋯N hydrogen-bonding inter­actions. The structure confirmed the identity of the compound as a reaction side product.

Related literature

For background information on the Groebke–Blackburn synthesis, see: Bienaymé & Bouzid (1998); Blackburn et al. (1998); Groebke et al. (1998); Mandair et al. (2002); Parchinsky et al. (2006). For the crystal structure of a similar compound, see: Wu et al. (2004). For information on graph-set notation to describe hydrogen-bonding motifs, see: Bernstein et al. (1995).

Experimental

Crystal data

• C₁₁H₁₀Br₂N₄

• M_r = 358.05

• Monoclinic, I 2/a

• a = 11.9075 (6) Å

• b = 4.0523 (2) Å

• c = 25.8065 (15) Å

• β = 98.326 (3)°

• V = 1232.11 (11) ų

• Z = 4

• Mo Kα radiation

• μ = 6.56 mm⁻¹

• T = 100 K

• 0.24 × 0.08 × 0.07 mm

Data collection

• Bruker Kappa APEXII DUO CCD diffractometer

• Absorption correction: numerical (SADABS; Sheldrick, 1996) T_min = 0.297, T_max = 0.675

• 11800 measured reflections

• 1903 independent reflections

• 1674 reflections with I > 2σ(I)

• R_int = 0.023

Refinement

• R[F² > 2σ(F²)] = 0.019

• wR(F²) = 0.051

• S = 1.03

• 1903 reflections

• 98 parameters

• 1 restraint

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

• Δρ_max = 0.70 e Å⁻³

• Δρ_min = −0.47 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2N⋯N1^i	0.87 (1)	2.11 (1)	2.9645 (18)	168 (2)
Symmetry code: (i) -x+1, -y+1, -z.

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXTL, publCIF (Westrip, 2010) and local programs.

Supporting information

S1. Comment

The Groebke-Blackburn reaction is the most popular way to prepare imidazo-azines from 2-aminoazines in a single-step. (Groebke et al., 1998; Bienaymé & Bouzid,1998; Blackburn et al., 1998). The reaction involves addition of 2-aminoazine 1 to the aldehyde in the presence of catalytic amounts of acid to generate the respective Schiff base which undergoes a non-concerted [4 + 1] cycloaddition with an isocyanide to form the imidazoazine 2 (Pathway A, Figure 1). Though imidazoazine 2 remained the major product, it was later found that the reaction also produced the isomeric imidazo[1,2-a]pyrimidine product 3 through an alternative iminium intermediate involving the ring nitrogen of 1 (Pathway B, Figure 1; Parchinsky et al., 2006). Similarly, nucleophilic solvents (for example, methanol) were found to promote interaction of the primary imine intermediate with the second molecule of 2-aminoazine or the solvent itself to give side-products like 4 (Pathway C, Figure 1; Mandair et al., 2002).

We, in one case, decided to synthesize N-benzyl-6-bromoindolizin-3-amine, 3a. Interestingly, the reaction did not yield the expected product 2a or the regioisomer 3a. However, the product which crystallized from a solution of dichloromethane turned out to be N,N'-bis(5-bromopyridin-2-yl)methanediamine, 4a in 20% yield (Figure 2).

The V-shaped structure of 4a is shown in Figure 3. The compound has crystallized with atom C6 on a twofold rotation axis, and has been set in space group I2/a. Molecular dimensions are unexceptional. In the crystal, inversion-related N—H···N hydrogen bonding interactions form an R²₂(8) graph set motif (Bernstein et al., 1995). As a result, the crystal forms an infinite hydrogen bonded tape of V-shaped molecules, which propagates in the a-axis direction. The tapes are stacked in the b-axis direction, and the separation between each tape is approximately 3.6 Å. The structure of the related compound N,N'-Di-2-pyridylmethylenediamine exhibits the same V-shaped structure, but with a different crystal packing arrangment (Wu et al., 2004).

Related literature

For background information on the Groebke–Blackburn synthesis, see: Bienaymé & Bouzid (1998); Blackburn et al. (1998); Groebke et al. (1998); Mandair et al. (2002); Parchinsky et al. (2006). For the crystal structure of a similar compound, see: Wu et al. (2004). For information on graph-set notation to describe hydrogen-bonding motifs, see: Bernstein et al. (1995).

S2. Experimental

To a solution of 5-bromopyridin-2-amine 1a (0.58 mmol, 100 mg) in dichloromethane (DCM) (1.5 ml), was added aq. 37% solution of formaldehyde (140 µl, 1.78 mmol) followed by (isocyanomethyl)benzene (75.4 µl, 0.58 mmol) and the solution was stirred for 10 min. DCM was evaporated and the resulting solid was irradiated under microwave at 100° C for 10 min. The crude product was purified through silica gel chromatography to provide 41 mg of 4a in (20% yield). The product was recrystallized from a DCM solution.

S3. Refinement

All H atoms were located in a difference map and are freely refined, with the exception of an N–H distance restaint of 0.88 (1) Å used on H2N. C–H distances lie in the range 0.92 (2) to 1.01 (2) Å.

The space group was set as I2/a since I2/a results in a smaller beta angle (and slightly shorter c axis).

Computing details

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), publCIF (Westrip, 2010) and local programs.

Figures

	Fig. 1. Three reaction pathways in the Groebke-Blackburn reaction.
	Fig. 2. Three possible products in the reaction described herein.
	Fig. 3. The molecular structure of 4a, with displacement ellipsoids at the 50% probability level. Unlabelled atoms are related to labelled atoms by a twofold rotation (symmetry operator: -x + 3/2, y, -z).
	Fig. 4. Hydrogen bonding interactions (blue dotted lines; red dotted lines indicate continuation) in the crystal structure of 4a. The long c axis has been truncated.

5-bromo-N-{[(5-bromopyridin-2-yl)amino]methyl}pyridin-2-amine

Crystal data

C11H10Br2N4	F(000) = 696
Mr = 358.05	Dx = 1.930 Mg m^−3
Monoclinic, I2/a	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -I 2ya	Cell parameters from 6689 reflections
a = 11.9075 (6) Å	θ = 3.2–30.6°
b = 4.0523 (2) Å	µ = 6.56 mm^−1
c = 25.8065 (15) Å	T = 100 K
β = 98.326 (3)°	Rod, colourless
V = 1232.11 (11) Å^3	0.24 × 0.08 × 0.07 mm
Z = 4

Data collection

Bruker Kappa APEXII DUO CCD diffractometer	1903 independent reflections
Radiation source: fine-focus sealed tube with Miracol optics	1674 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.023
ϕ and ω scans	θmax = 30.7°, θmin = 1.6°
Absorption correction: numerical (SADABS; Sheldrick, 1996)	h = −16→17
Tmin = 0.297, Tmax = 0.675	k = −5→5
11800 measured reflections	l = −36→37

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.019	Hydrogen site location: difference Fourier map
wR(F^2) = 0.051	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0253P)^2 + 1.5219P] where P = (Fo^2 + 2Fc^2)/3
1903 reflections	(Δ/σ)max = 0.002
98 parameters	Δρmax = 0.70 e Å^−3
1 restraint	Δρmin = −0.47 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
Br	0.596053 (15)	1.07921 (4)	0.214841 (6)	0.02877 (6)
N1	0.54707 (10)	0.7010 (3)	0.06616 (5)	0.0220 (2)
N2	0.65505 (10)	0.4435 (3)	0.01189 (5)	0.0213 (2)
H2N	0.5900 (11)	0.412 (5)	−0.0074 (7)	0.026 (5)*
C1	0.64953 (12)	0.5832 (4)	0.05935 (6)	0.0189 (3)
C2	0.74416 (12)	0.6124 (4)	0.09880 (6)	0.0205 (3)
H2	0.8137 (17)	0.536 (5)	0.0930 (8)	0.025 (5)*
C3	0.73085 (13)	0.7578 (4)	0.14580 (6)	0.0224 (3)
H3	0.7917 (16)	0.776 (5)	0.1733 (8)	0.026 (5)*
C4	0.62425 (13)	0.8776 (4)	0.15222 (6)	0.0218 (3)
C5	0.53646 (13)	0.8461 (4)	0.11167 (6)	0.0231 (3)
H5	0.4625 (18)	0.923 (5)	0.1152 (9)	0.030 (6)*
C6	0.7500	0.2511 (5)	0.0000	0.0207 (4)
H6	0.7804 (16)	0.108 (5)	0.0309 (8)	0.024 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Br	0.04319 (11)	0.02711 (9)	0.01784 (8)	−0.00538 (7)	0.01056 (6)	−0.00376 (6)
N1	0.0194 (5)	0.0262 (6)	0.0208 (6)	−0.0010 (5)	0.0045 (4)	−0.0038 (5)
N2	0.0166 (5)	0.0286 (6)	0.0188 (6)	−0.0013 (5)	0.0033 (4)	−0.0050 (5)
C1	0.0201 (6)	0.0198 (6)	0.0175 (6)	−0.0032 (5)	0.0052 (5)	0.0006 (5)
C2	0.0192 (6)	0.0231 (7)	0.0192 (6)	−0.0013 (5)	0.0030 (5)	0.0023 (5)
C3	0.0258 (7)	0.0232 (7)	0.0176 (6)	−0.0029 (6)	0.0010 (5)	0.0026 (6)
C4	0.0294 (7)	0.0214 (6)	0.0159 (6)	−0.0049 (5)	0.0074 (5)	−0.0013 (5)
C5	0.0224 (7)	0.0260 (7)	0.0219 (7)	−0.0020 (6)	0.0071 (5)	−0.0032 (6)
C6	0.0227 (9)	0.0204 (9)	0.0199 (9)	0.000	0.0067 (7)	0.000

Geometric parameters (Å, º)

Br—C4	1.8838 (15)	C2—C3	1.378 (2)
N1—C1	1.3452 (19)	C3—H3	0.94 (2)
N1—C5	1.3356 (19)	C3—C4	1.391 (2)
N2—H2N	0.868 (9)	C4—C5	1.374 (2)
N2—C1	1.3596 (18)	C5—H5	0.95 (2)
N2—C6	1.4425 (17)	C6—N2^i	1.4425 (17)
C1—C2	1.410 (2)	C6—H6	1.01 (2)
C2—H2	0.92 (2)
C1—N1—C5	118.31 (13)	C2—C3—C4	118.51 (14)
H2N—N2—C1	115.0 (14)	H3—C3—C4	119.9 (13)
H2N—N2—C6	117.5 (14)	Br—C4—C3	122.18 (11)
C1—N2—C6	123.94 (11)	Br—C4—C5	118.90 (12)
N1—C1—N2	115.37 (13)	C3—C4—C5	118.92 (14)
N1—C1—C2	121.41 (13)	N1—C5—C4	123.52 (14)
N2—C1—C2	123.20 (13)	N1—C5—H5	115.8 (13)
C1—C2—H2	120.1 (13)	C4—C5—H5	120.6 (13)
C1—C2—C3	119.31 (14)	N2—C6—N2^i	114.56 (18)
H2—C2—C3	120.6 (13)	N2—C6—H6	110.2 (11)
C2—C3—H3	121.6 (13)	N2^i—C6—H6	106.1 (11)
C5—N1—C1—N2	−178.95 (14)	C2—C3—C4—Br	179.74 (11)
C5—N1—C1—C2	−0.4 (2)	C2—C3—C4—C5	0.1 (2)
C6—N2—C1—N1	−168.30 (15)	C1—N1—C5—C4	−0.9 (2)
C6—N2—C1—C2	13.2 (2)	Br—C4—C5—N1	−178.55 (12)
N1—C1—C2—C3	1.6 (2)	C3—C4—C5—N1	1.1 (2)
N2—C1—C2—C3	179.98 (14)	C1—N2—C6—N2^i	−80.54 (14)
C1—C2—C3—C4	−1.4 (2)

Symmetry code: (i) −x+3/2, y, −z.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···N1^ii	0.87 (1)	2.11 (1)	2.9645 (18)	168 (2)

Symmetry code: (ii) −x+1, −y+1, −z.