2-[(E)-(6-Amino-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidin-5-yl)imino­meth­yl]pyridinium bromide

Irvin Booysen; Muhammed Ismail; Thomas Gerber; Eric Hosten; Richard Betz

doi:10.1107/S1600536811033290

. 2011 Aug 27;67(Pt 9):o2387–o2388. doi: 10.1107/S1600536811033290

2-[(E)-(6-Amino-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)iminomethyl]pyridinium bromide

Irvin Booysen ^a, Muhammed Ismail ^a, Thomas Gerber ^b, Eric Hosten ^b, Richard Betz ^b,^*

PMCID: PMC3200889 PMID: 22065608

Abstract

The title compound, C₁₂H₁₄N₅O₂ ⁺·Br⁻, is the hydrobromide salt of a Schiff base in which protonation has taken place at the pyridine N atom. This organic cation is essentially planar (r.m.s. of all fitted non-H atoms = 0.0448 Å). In the crystal, N—H⋯Br hydrogen bonds as well as C—H⋯O and C–H⋯Br interactions connect the molecules, forming a three-dimensional network.

Related literature

For the development of radiopharmaceuticals, see: Gerber et al. (2011 ▶). For the crystal structure of the neutral organic parent molecule, see: Booysen et al. (2011a ▶). For the crystal structures of polymorphs of 6-amino-1,3-dimethyl-5-[(E-2-(methylsulfanyl)benzylideneamino]pyrimidine-2,4(1H,3H)-dione, see: Booysen et al. (2011b ▶,c ▶). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶).

Experimental

Crystal data

C₁₂H₁₄N₅O₂ ⁺·Br⁻
M _r = 340.19
Monoclinic,
a = 8.9520 (2) Å
b = 4.9630 (1) Å
c = 30.9123 (6) Å
β = 105.391 (1)°
V = 1324.14 (5) Å³
Z = 4
Mo Kα radiation
μ = 3.11 mm⁻¹
T = 200 K
0.55 × 0.28 × 0.12 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T _min = 0.660, T _max = 1.000
10606 measured reflections
3277 independent reflections
2998 reflections with I > 2σ(I)
R _int = 0.017

Refinement

R[F ² > 2σ(F ²)] = 0.029
wR(F ²) = 0.068
S = 1.16
3277 reflections
195 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.42 e Å⁻³
Δρ_min = −0.36 e Å⁻³

Data collection: APEX2 (Bruker, 2010 ▶); cell refinement: SAINT (Bruker, 2010 ▶); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811033290/su2307sup1.cif

e-67-o2387-sup1.cif^{(17.2KB, cif)}

Supplementary material file. DOI: 10.1107/S1600536811033290/su2307Isup2.cdx

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811033290/su2307Isup3.hkl

e-67-o2387-Isup3.hkl^{(160.8KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811033290/su2307Isup4.cml

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H741⋯Br1ⁱ	0.87 (3)	2.77 (3)	3.4584 (19)	138 (2)
N4—H742⋯Br1ⁱⁱ	0.82 (3)	2.55 (3)	3.312 (2)	154 (2)
N5—H751⋯Br1ⁱⁱ	0.85 (3)	2.41 (3)	3.1763 (18)	151 (2)
C5—H5A⋯Br1ⁱ	0.98	2.89	3.764 (2)	148
C6—H6A⋯O1ⁱⁱⁱ	0.98	2.60	3.453 (3)	145
C9—H9⋯O2^iv	0.95	2.53	3.446 (3)	162
C10—H10⋯O1^v	0.95	2.56	3.429 (3)	152

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) .

Acknowledgments

The authors thank Ms Dakota Neale-Shutte for helpful discussions.

supplementary crystallographic information

Comment

Next to cardiovascular diseases, cancer has become one of the main fatal diseases in industrialized countries. Apart from classical surgery, chemo- and radiotherapeutic treatments have entered the arsenal of possible cures for certain types of cancer. All methods, however, suffer from their own set of problematic side-effects and, as a consequence, the development of radiopharmaceuticals – combining the advantages of chemotherapy as well as radiation methods while at the same time avoiding their unique respective undesired side-effects – has been a topic of research (Gerber et al., 2011). Tailoring and fine-tuning of the envisioned radiopharmaceuticals' properties such as lipophilicity and, in particular, inertness is of paramount importance with respect to possible future in vivo applications in contemporary medicine and requires sound knowledge about structural parameters of the ligands applied if a more heuristic approach in the synthesis is to triumph over pure trial-and-error as it is encountered in this specific field of coordination chemistry up to the present day. To allow for an assessment of changes in structural features upon coordination, the molecular and crystal structure of the title compound has been determined. The crystal structure of the neutral compound (Booysen et al., 2011a), and other 6-amino-1,3-dimethyl-2,4(1H,3H)-dione-derived Schiff-base ligands (Booysen et al., 2011b,c), have been described previously.

The molecular structure of the title molecule is illustrated in Fig. 1. Protonation of the neutral organic ligand took place on the nitrogen atom, N5, of the pyridine moiety. The molecule has the E configuration about the C=N bond. As expected the intracyclic angles in the protonated pyridine moiety cover a range of 118.09 (19)–123.33 (19) °, with the largest angle on the protonated nitrogen atom, N, and the smallest angle on the carbon atom, C , bonded to the exocyclic substituent. The organic cation is essentially planar (r.m.s. for all its fitted non-hydrogen atoms = 0.0448 Å).

In the crystal, N-H···Br hydrogen bonds as well as C–H···O and C–H···Br contacts are observed (Table 1). While the hydrogen bonds are formed between the nitrogen-bonded hydrogen atoms and the bromide anion exclusively, the C–H···O contacts involve the hydrogen atoms of the pyridine moiety and one of the nitrogen-bonded methyl groups as donors and both oxygen atoms as acceptors. The C–H···Br contact is supported by one of the hydrogen atoms of the second nitrogen-bonded methyl group. In terms of graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptor for the classical hydrogen bonds is DDD on the unitary level, whereas the C–H···O contacts necessitate a C(5)C(8)C(11) on the same level. In total, these contact result in the formation of a three-dimensional network (Fig. 3).

Experimental

The title compound was prepared by the reaction of (E)-6-amino-1,3- dimethyl-5-(pyridin-2-ylmethyleneamino)pyrimidine-2,4(1H,3H)- dione and trans-[ReOBr₃(PPh₃)₂] in methanol. The solution was filtered and single crystals suitable for the X-ray analysis were obtained from the mother liquor which was left in a fridge for several days.