Metal–nucleobase inter­action: bis[4-amino­pyrimidin-2(1H)-one-κN 3]dibromidozinc(II)

Ammasai Karthikeyan; Samuel Ebenezer; Packianathan Thomas Muthiah

doi:10.1107/S1600536810049305

. 2010 Nov 30;66(Pt 12):m1693. doi: 10.1107/S1600536810049305

Metal–nucleobase interaction: bis[4-aminopyrimidin-2(1H)-one-κN ³]dibromidozinc(II)

Ammasai Karthikeyan ^a, Samuel Ebenezer ^a, Packianathan Thomas Muthiah ^a,^*

PMCID: PMC3011690 PMID: 21589348

Abstract

In the title complex, [ZnBr₂(C₄H₅N₃O)₂], the central metal ion is coordinated to two bromide ions and endocyclic N atoms of the two cytosine molecules leading to a distorted tetrahedral geometry. The structure is isotypic with [CdBr₂(C₄H₅N₃O)₂] [Muthiah et al. (2001). Acta Cryst. E57, m558–m560]. There are two interligand N—H⋯Br hydrogen bonds, generating two hydrogen-bonded rings stabilizing the coordination sphere. The complex aggregates, forming supramolecular chains, sheets and staircases through N—H⋯O and N—H⋯Br hydrogen bonding and π–π stacking interactions [centroid–centroid distance = 3.616 (2) Å].

Related literature

For metal ion–nucleic acid interactions, see: Muller (2010 ▶). For different modes of binding between metal ions and cytosine, see: Lippert (2000 ▶). For an isotypic complex, see: Muthiah et al. (2001 ▶).

Experimental

Crystal data

[ZnBr₂(C₄H₅N₃O)₂]
M _r = 447.41
Triclinic,
a = 7.1337 (2) Å
b = 7.8375 (2) Å
c = 12.4275 (3) Å
α = 86.746 (2)°
β = 75.199 (2)°
γ = 87.448 (2)°
V = 670.36 (3) Å³
Z = 2
Mo Kα radiation
μ = 7.80 mm⁻¹
T = 293 K
0.3 × 0.2 × 0.2 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T _min = 0.203, T _max = 0.305
13254 measured reflections
2973 independent reflections
2204 reflections with I > 2σ(I)
R _int = 0.043

Refinement

R[F ² > 2σ(F ²)] = 0.036
wR(F ²) = 0.083
S = 1.02
2973 reflections
172 parameters
H-atom parameters constrained
Δρ_max = 0.69 e Å⁻³
Δρ_min = −0.44 e Å⁻³

Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶); data reduction: SAINT; program(s) used to solve structure: SIR92 (Altomare et al., 1993 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶); software used to prepare material for publication: PLATON.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810049305/hg2756sup1.cif

e-66-m1693-sup1.cif^{(21KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810049305/hg2756Isup2.hkl

e-66-m1693-Isup2.hkl^{(142.9KB, hkl)}

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
N1A—H1A⋯O2Aⁱ	0.86	1.94	2.766 (5)	161
N1B—H1B⋯Br1ⁱⁱ	0.86	2.70	3.483 (3)	151
N4A—H2A⋯Br1	0.86	2.74	3.577 (4)	165
N4B—H2B⋯Br2	0.86	2.65	3.454 (3)	155
N4A—H3A⋯Br2ⁱⁱⁱ	0.86	2.91	3.339 (4)	112
N4B—H3B⋯O2B^iv	0.86	2.19	3.003 (5)	157
C5A—H5A⋯Br2^v	0.93	2.87	3.726 (4)	153
C6A—H6A⋯O2B^vi	0.93	2.42	3.292 (6)	156

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

Acknowledgments

The authors thank the DST–India (FIST programme) for the use of the diffractometer at the School of Chemistry, Bharathidasan University.

supplementary crystallographic information

Comment

The studies of metal ion–nucleic acid interactions are of continued interest in bioinorganic chemistry (Muller, 2010). There are several modes of binding between a cytosine and metal ion. The cytosine coordinates in a monodentate fashion either through N3, N4, O2 or C5 sites. Similarly it acts as a bidentate ligand by chelating, semi-chelating or bridging via N3, O2 and N3, N4 sites (Lippert, 2000). However the most preferable mode of binding is via N3 as observed in majority of the cases. In the present study we have prepared a metal complex of zinc-cytosine as a model for Zn (II) ion interactions with guanine-cytosine rich regions of nucleic acids (DNA and RNA). The crystal structure is found to be isomorphous with the earlier reported structure of dibromobis(cytosine)cadmium(II) (Muthiah et al., 2001).

The title complex is coordinated by two bromide ions in addition to two cytosine molecules. The ORTEP view is shown in Figure 1. The two crystallographically independent cytosine molecules coordinate through N3 position forming a tetrahedral geometry around the central Zn (II) ion with slight distortion. This distortion is not only because of the dissimilar ligands coordinated to the central metal ion but is due to the additional attraction between the zinc ion and the oxygen of the cytosine molecule. This can be confirmed by looking into the contact distances between Zn···O in both the molecules (A and B) which are 2.804 (3) Å and 2.858 (3) Å respectively. It is further substantiated by the exocyclic bond angles at N3 (Zn—N3—C4 and Zn—N3—C2) of cytosine which is 132.0 (3)° and 109.0 (3)° for molecule A and 128.1 (3)° and 109.3 (2)° for molecule B. The stability of the coordinated metal complex is also enhanced by the two inter-ligand hydrogen bonds (N—H···Br hydrogen bond). These are formed between the amino group of the coordinated cytosine and the coordinated bromide ion which are lying in proximity. The interligand hydrogen bonds generate two hydrogen-bonded rings (Figure 1). These are very characteristic of metal-nucleobase interactions (Lippert, 2000).

The hydrogen bonding geometries of the title complex are given in Table 1. The two cytosines that have coordinated to the metal ion, although look similar, form different inter-molecular hydrogen bonds. The amino nitrogen of molecule B connects with the oxygen of the neighboring molecule via N4B—H4B···O2B extending into an infinite chain. This chain is supported by an additional weak hydrogen bond (N4A-H4A2···Br2) between the A molecules of neighboring cytosine (Figure 2). The infinite chain can further aggregate itself in two different ways. A supramolecular sheet is formed when the adjacent chains are linked by molecule B via N1B—H1B···Br1 hydrogen bonds (Figure 3). Similarly a staircase is formed when the inversely related chains pair up via N1A—H1A···O2A hydrogen bonds involving molecule A (Figure 4). These molecules form the steps of the staircase and stack one over the other through π-π stacking with a cg-cg distance of 3.616 (2) and a slip angle of 24.32°. Besides this, weak C—H···O and C—H···Br interactions are additionally present which stabilize the entire crystal structure.

Experimental

Solution of zinc bromide anhydrous (0.056 g, 0.25 mmol) in 10 ml of hot propanol and cytosine (0.055 g, 0.50 mmol) in 10 ml of hot water were mixed mixed and dissolved in an 1:2 molar ratio. The resultant solution was heated over a water bath for an hour and on slow cooling the solution gave transparent colourless prismatic crystals.