organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

aDepartment of Chemistry and Biochemistry, 1306 E University Boulevard, The University of Arizona, Tucson, AZ 85721, USA, and bSouthwest Center for Drug Discovery, College of Pharmacy, The University of Arizona, Tucson, AZ 85737, USA
*Correspondence e-mail: gsnichol@email.arizona.edu

(Received 22 February 2011; accepted 3 March 2011; online 9 March 2011)

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[Bienaymé, H. & Bouzid, K. (1998). Angew. Chem. Int. Ed. 37, 2234-2237.]); Blackburn et al. (1998[Blackburn, C., Guan, B., Fleming, P., Shiosaki, K. & Tsai, S. (1998). Tetrahedron Lett. 39, 3635-3638.]); Groebke et al. (1998[Groebke, K., Weber, L. & Mehlin, F. (1998). Synlett, pp. 661-663.]); Mandair et al. (2002[Mandair, G. S., Light, M., Russell, A., Hursthouse, M. & Bradley, M. (2002). Tetrahedron Lett. 43, 4267-4269.]); Parchinsky et al. (2006[Parchinsky, V. Z., Schuvalova, O., Ushalova, O., Krachenko, D. V. & Krasavin, M. (2006). Tetrahedron Lett. 47, 947-951.]). For the crystal structure of a similar compound, see: Wu et al. (2004[Wu, H., Zhou, J., Yu, H.-Z., Lu, L.-L., Xu, Z., Yu, K.-B. & Shi, D.-Q. (2004). Acta Cryst. E60, o2085-o2086.]). For information on graph-set notation to describe hydrogen-bonding motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C11H10Br2N4

  • Mr = 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) Å3

  • 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[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.297, Tmax = 0.675

  • 11800 measured reflections

  • 1903 independent reflections

  • 1674 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.70 e Å−3

  • Δρmin = −0.47 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2N⋯N1i 0.87 (1) 2.11 (1) 2.9645 (18) 168 (2)
Symmetry code: (i) -x+1, -y+1, -z.

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: SHELXTL, publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]) and local programs.

Supporting information


Comment top

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 top

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 top

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.

Refinement top

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 top

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 top
[Figure 1] Fig. 1. Three reaction pathways in the Groebke-Blackburn reaction.
[Figure 2] Fig. 2. Three possible products in the reaction described herein.
[Figure 3] 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).
[Figure 4] 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 top
Crystal data top
C11H10Br2N4F(000) = 696
Mr = 358.05Dx = 1.930 Mg m3
Monoclinic, I2/aMo Kα radiation, λ = 0.71073 Å
Hall symbol: -I 2yaCell parameters from 6689 reflections
a = 11.9075 (6) Åθ = 3.2–30.6°
b = 4.0523 (2) ŵ = 6.56 mm1
c = 25.8065 (15) ÅT = 100 K
β = 98.326 (3)°Rod, colourless
V = 1232.11 (11) Å30.24 × 0.08 × 0.07 mm
Z = 4
Data collection top
Bruker Kappa APEXII DUO CCD
diffractometer
1903 independent reflections
Radiation source: fine-focus sealed tube with Miracol optics1674 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.023
ϕ and ω scansθmax = 30.7°, θmin = 1.6°
Absorption correction: numerical
(SADABS; Sheldrick, 1996)
h = 1617
Tmin = 0.297, Tmax = 0.675k = 55
11800 measured reflectionsl = 3637
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.019Hydrogen site location: difference Fourier map
wR(F2) = 0.051H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0253P)2 + 1.5219P]
where P = (Fo2 + 2Fc2)/3
1903 reflections(Δ/σ)max = 0.002
98 parametersΔρmax = 0.70 e Å3
1 restraintΔρmin = 0.47 e Å3
Crystal data top
C11H10Br2N4V = 1232.11 (11) Å3
Mr = 358.05Z = 4
Monoclinic, I2/aMo Kα radiation
a = 11.9075 (6) ŵ = 6.56 mm1
b = 4.0523 (2) ÅT = 100 K
c = 25.8065 (15) Å0.24 × 0.08 × 0.07 mm
β = 98.326 (3)°
Data collection top
Bruker Kappa APEXII DUO CCD
diffractometer
1903 independent reflections
Absorption correction: numerical
(SADABS; Sheldrick, 1996)
1674 reflections with I > 2σ(I)
Tmin = 0.297, Tmax = 0.675Rint = 0.023
11800 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0191 restraint
wR(F2) = 0.051H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.70 e Å3
1903 reflectionsΔρmin = 0.47 e Å3
98 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
xyzUiso*/Ueq
Br0.596053 (15)1.07921 (4)0.214841 (6)0.02877 (6)
N10.54707 (10)0.7010 (3)0.06616 (5)0.0220 (2)
N20.65505 (10)0.4435 (3)0.01189 (5)0.0213 (2)
H2N0.5900 (11)0.412 (5)0.0074 (7)0.026 (5)*
C10.64953 (12)0.5832 (4)0.05935 (6)0.0189 (3)
C20.74416 (12)0.6124 (4)0.09880 (6)0.0205 (3)
H20.8137 (17)0.536 (5)0.0930 (8)0.025 (5)*
C30.73085 (13)0.7578 (4)0.14580 (6)0.0224 (3)
H30.7917 (16)0.776 (5)0.1733 (8)0.026 (5)*
C40.62425 (13)0.8776 (4)0.15222 (6)0.0218 (3)
C50.53646 (13)0.8461 (4)0.11167 (6)0.0231 (3)
H50.4625 (18)0.923 (5)0.1152 (9)0.030 (6)*
C60.75000.2511 (5)0.00000.0207 (4)
H60.7804 (16)0.108 (5)0.0309 (8)0.024 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br0.04319 (11)0.02711 (9)0.01784 (8)0.00538 (7)0.01056 (6)0.00376 (6)
N10.0194 (5)0.0262 (6)0.0208 (6)0.0010 (5)0.0045 (4)0.0038 (5)
N20.0166 (5)0.0286 (6)0.0188 (6)0.0013 (5)0.0033 (4)0.0050 (5)
C10.0201 (6)0.0198 (6)0.0175 (6)0.0032 (5)0.0052 (5)0.0006 (5)
C20.0192 (6)0.0231 (7)0.0192 (6)0.0013 (5)0.0030 (5)0.0023 (5)
C30.0258 (7)0.0232 (7)0.0176 (6)0.0029 (6)0.0010 (5)0.0026 (6)
C40.0294 (7)0.0214 (6)0.0159 (6)0.0049 (5)0.0074 (5)0.0013 (5)
C50.0224 (7)0.0260 (7)0.0219 (7)0.0020 (6)0.0071 (5)0.0032 (6)
C60.0227 (9)0.0204 (9)0.0199 (9)0.0000.0067 (7)0.000
Geometric parameters (Å, º) top
Br—C41.8838 (15)C2—C31.378 (2)
N1—C11.3452 (19)C3—H30.94 (2)
N1—C51.3356 (19)C3—C41.391 (2)
N2—H2N0.868 (9)C4—C51.374 (2)
N2—C11.3596 (18)C5—H50.95 (2)
N2—C61.4425 (17)C6—N2i1.4425 (17)
C1—C21.410 (2)C6—H61.01 (2)
C2—H20.92 (2)
C1—N1—C5118.31 (13)C2—C3—C4118.51 (14)
H2N—N2—C1115.0 (14)H3—C3—C4119.9 (13)
H2N—N2—C6117.5 (14)Br—C4—C3122.18 (11)
C1—N2—C6123.94 (11)Br—C4—C5118.90 (12)
N1—C1—N2115.37 (13)C3—C4—C5118.92 (14)
N1—C1—C2121.41 (13)N1—C5—C4123.52 (14)
N2—C1—C2123.20 (13)N1—C5—H5115.8 (13)
C1—C2—H2120.1 (13)C4—C5—H5120.6 (13)
C1—C2—C3119.31 (14)N2—C6—N2i114.56 (18)
H2—C2—C3120.6 (13)N2—C6—H6110.2 (11)
C2—C3—H3121.6 (13)N2i—C6—H6106.1 (11)
C5—N1—C1—N2178.95 (14)C2—C3—C4—Br179.74 (11)
C5—N1—C1—C20.4 (2)C2—C3—C4—C50.1 (2)
C6—N2—C1—N1168.30 (15)C1—N1—C5—C40.9 (2)
C6—N2—C1—C213.2 (2)Br—C4—C5—N1178.55 (12)
N1—C1—C2—C31.6 (2)C3—C4—C5—N11.1 (2)
N2—C1—C2—C3179.98 (14)C1—N2—C6—N2i80.54 (14)
C1—C2—C3—C41.4 (2)
Symmetry code: (i) x+3/2, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···N1ii0.87 (1)2.11 (1)2.9645 (18)168 (2)
Symmetry code: (ii) x+1, y+1, z.

Experimental details

Crystal data
Chemical formulaC11H10Br2N4
Mr358.05
Crystal system, space groupMonoclinic, I2/a
Temperature (K)100
a, b, c (Å)11.9075 (6), 4.0523 (2), 25.8065 (15)
β (°) 98.326 (3)
V3)1232.11 (11)
Z4
Radiation typeMo Kα
µ (mm1)6.56
Crystal size (mm)0.24 × 0.08 × 0.07
Data collection
DiffractometerBruker Kappa APEXII DUO CCD
diffractometer
Absorption correctionNumerical
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.297, 0.675
No. of measured, independent and
observed [I > 2σ(I)] reflections
11800, 1903, 1674
Rint0.023
(sin θ/λ)max1)0.718
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.019, 0.051, 1.03
No. of reflections1903
No. of parameters98
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.70, 0.47

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), ORTEP-3 for Windows (Farrugia, 1997), SHELXTL (Sheldrick, 2008), publCIF (Westrip, 2010) and local programs.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···N1i0.868 (9)2.111 (10)2.9645 (18)168 (2)
Symmetry code: (i) x+1, y+1, z.
 

Acknowledgements

The diffractometer was purchased with funding from NSF grant CHE-0741837.

References

First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science
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First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals
First citationWu, H., Zhou, J., Yu, H.-Z., Lu, L.-L., Xu, Z., Yu, K.-B. & Shi, D.-Q. (2004). Acta Cryst. E60, o2085–o2086.  Web of Science CSD CrossRef IUCr Journals

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