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Acta Crystallogr Sect E Struct Rep Online. 2010 December 1; 66(Pt 12): m1693.
Published online 2010 November 30. doi:  10.1107/S1600536810049305
PMCID: PMC3011690

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

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 [triangle]). For different modes of binding between metal ions and cytosine, see: Lippert (2000 [triangle]). For an isotypic complex, see: Muthiah et al. (2001 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-m1693-scheme1.jpg

Experimental

Crystal data

  • [ZnBr2(C4H5N3O)2]
  • M r = 447.41
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-m1693-efi1.jpg
  • 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 [triangle]) 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
  • Δρmax = 0.69 e Å−3
  • Δρmin = −0.44 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

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

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.

Refinement

All hydrogen atoms were positioned geometrically and were refined using a riding model. The N—H and C—H bond lengths are 0.86 and 0.93 Å respectively [Uiso(H)=1.2 Ueq (parent atom)].

Figures

Fig. 1.
The asymmetric unit of (I), showing 50% probability displacement ellipsoids. Dashed lines indicate hydrogen bonds.
Fig. 2.
View of an infinite chain linked by N4B—H4B···O2B and N4A-H4A2···Br2 hydrogen bonds.
Fig. 3.
View of a supramolecular sheet along the (001) plane.
Fig. 4.
Molecular staircase formed by pairing of two infinite chains through hydrogen bonding and stacking interactions.

Crystal data

[ZnBr2(C4H5N3O)2]Z = 2
Mr = 447.41F(000) = 432
Triclinic, P1Dx = 2.217 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.1337 (2) ÅCell parameters from 2973 reflections
b = 7.8375 (2) Åθ = 1.7–27.2°
c = 12.4275 (3) ŵ = 7.80 mm1
α = 86.746 (2)°T = 293 K
β = 75.199 (2)°Prism, colourless
γ = 87.448 (2)°0.3 × 0.2 × 0.2 mm
V = 670.36 (3) Å3

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2973 independent reflections
Radiation source: fine-focus sealed tube2204 reflections with I > 2σ(I)
graphiteRint = 0.043
[var phi] and ω scansθmax = 27.2°, θmin = 1.7°
Absorption correction: multi-scan (SADABS; Bruker, 2008)h = −9→9
Tmin = 0.203, Tmax = 0.305k = −10→10
13254 measured reflectionsl = −15→15

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.083H-atom parameters constrained
S = 1.02w = 1/[σ2(Fo2) + (0.0441P)2] where P = (Fo2 + 2Fc2)/3
2973 reflections(Δ/σ)max = 0.001
172 parametersΔρmax = 0.69 e Å3
0 restraintsΔρmin = −0.44 e Å3

Special details

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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)

xyzUiso*/Ueq
Br10.34971 (6)1.00965 (5)0.84763 (4)0.0378 (1)
Br20.88031 (6)1.05932 (5)0.68592 (4)0.0374 (1)
Zn0.63076 (7)0.84924 (6)0.74430 (4)0.0303 (2)
O2A0.9020 (4)0.6403 (4)0.6017 (3)0.0454 (11)
O2B0.4019 (4)0.5579 (3)0.8291 (3)0.0372 (10)
N1A0.7973 (5)0.6009 (4)0.4478 (3)0.0326 (11)
N1B0.5996 (5)0.3618 (4)0.8891 (3)0.0364 (11)
N3A0.6105 (4)0.7588 (4)0.5954 (3)0.0275 (10)
N3B0.6990 (4)0.6425 (4)0.8371 (3)0.0264 (10)
N4A0.3118 (5)0.8664 (4)0.5860 (3)0.0426 (12)
N4B1.0054 (5)0.7147 (4)0.8420 (3)0.0439 (14)
C2A0.7755 (6)0.6643 (5)0.5505 (4)0.0304 (12)
C2B0.5592 (6)0.5230 (5)0.8506 (3)0.0296 (12)
C4A0.4734 (6)0.7811 (5)0.5385 (4)0.0307 (14)
C4B0.8725 (6)0.5973 (5)0.8562 (3)0.0283 (12)
C5A0.4985 (6)0.7156 (5)0.4323 (4)0.0367 (16)
C5B0.9146 (6)0.4288 (5)0.8921 (4)0.0352 (12)
C6A0.6632 (6)0.6267 (5)0.3895 (4)0.0371 (16)
C6B0.7763 (7)0.3150 (5)0.9073 (4)0.0396 (16)
H1A0.901100.542100.419300.0390*
H1B0.510600.287300.902400.0430*
H2A0.297200.905400.651100.0510*
H2B0.980300.817700.821000.0530*
H3A0.221300.882900.551900.0510*
H3B1.116900.687900.853800.0530*
H5A0.403900.733500.393100.0440*
H5B1.035000.398600.904700.0420*
H6A0.684500.582800.319200.0450*
H6B0.799900.202900.930400.0480*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Br10.0296 (2)0.0316 (2)0.0490 (3)−0.0027 (2)−0.0031 (2)−0.0055 (2)
Br20.0269 (2)0.0323 (2)0.0511 (3)−0.0019 (2)−0.0075 (2)0.0042 (2)
Zn0.0284 (3)0.0287 (2)0.0348 (3)0.0000 (2)−0.0101 (2)−0.0002 (2)
O2A0.0353 (18)0.060 (2)0.047 (2)0.0205 (15)−0.0223 (16)−0.0176 (16)
O2B0.0288 (17)0.0358 (16)0.0495 (19)−0.0045 (13)−0.0135 (14)−0.0045 (14)
N1A0.0248 (19)0.0391 (19)0.035 (2)0.0063 (15)−0.0093 (16)−0.0096 (16)
N1B0.039 (2)0.0251 (17)0.045 (2)−0.0093 (16)−0.0100 (18)0.0027 (16)
N3A0.0233 (18)0.0268 (16)0.0331 (19)0.0014 (14)−0.0089 (15)−0.0022 (15)
N3B0.0229 (18)0.0254 (16)0.0319 (19)−0.0029 (14)−0.0092 (15)0.0026 (14)
N4A0.032 (2)0.050 (2)0.050 (2)0.0118 (18)−0.0187 (19)−0.0110 (19)
N4B0.033 (2)0.044 (2)0.061 (3)−0.0100 (17)−0.0259 (19)0.0166 (19)
C2A0.028 (2)0.030 (2)0.034 (2)0.0022 (18)−0.0098 (19)−0.0019 (18)
C2B0.028 (2)0.030 (2)0.029 (2)−0.0046 (18)−0.0031 (18)−0.0025 (18)
C4A0.029 (2)0.0242 (19)0.039 (3)−0.0022 (17)−0.0098 (19)0.0035 (18)
C4B0.030 (2)0.032 (2)0.023 (2)−0.0017 (18)−0.0074 (17)0.0017 (17)
C5A0.038 (3)0.037 (2)0.041 (3)0.002 (2)−0.022 (2)0.001 (2)
C5B0.035 (2)0.039 (2)0.035 (2)0.002 (2)−0.016 (2)−0.001 (2)
C6A0.039 (3)0.039 (2)0.035 (3)0.000 (2)−0.012 (2)−0.005 (2)
C6B0.051 (3)0.031 (2)0.038 (3)0.003 (2)−0.015 (2)0.002 (2)

Geometric parameters (Å, °)

Br1—Zn2.4275 (7)N4B—C4B1.323 (5)
Br2—Zn2.4232 (7)N1A—H1A0.8600
Zn—N3A2.060 (4)N1B—H1B0.8600
Zn—N3B2.049 (3)N4A—H3A0.8600
O2A—C2A1.233 (6)N4A—H2A0.8600
O2B—C2B1.234 (5)N4B—H2B0.8600
N1A—C2A1.365 (6)N4B—H3B0.8600
N1A—C6A1.342 (6)C4A—C5A1.409 (7)
N1B—C2B1.370 (5)C4B—C5B1.414 (6)
N1B—C6B1.367 (6)C5A—C6A1.341 (6)
N3A—C2A1.371 (5)C5B—C6B1.330 (6)
N3A—C4A1.346 (6)C5A—H5A0.9300
N3B—C2B1.371 (5)C5B—H5B0.9300
N3B—C4B1.347 (5)C6A—H6A0.9300
N4A—C4A1.324 (6)C6B—H6B0.9300
Br1···Br23.8306 (7)N4A···Br2ii3.339 (4)
Br1···O2B3.558 (2)N4A···C4Aiii3.325 (5)
Br1···N1Bi3.483 (3)N4B···Br1iv3.463 (3)
Br1···N4A3.577 (4)N4B···Br23.454 (3)
Br1···N4Bii3.463 (3)N4B···O2Biv3.003 (5)
Br2···C5Aiii3.726 (4)C2B···C6Bv3.588 (6)
Br2···N4Aiv3.339 (4)C2B···N1Bv3.306 (5)
Br2···N4B3.454 (3)C2B···C2Bv3.592 (5)
Br2···C6Bi3.404 (5)C4A···C6Avii3.387 (6)
Br2···N3A3.511 (3)C4A···N4Aiii3.325 (5)
Br2···Br13.8306 (7)C4A···C4Aiii3.520 (6)
Br2···O2A3.488 (3)C4B···O2A3.116 (5)
Br1···H6Bv3.1100C5A···N1Avii3.357 (5)
Br1···H2A2.7400C5A···Br2iii3.726 (4)
Br1···H2Bii3.1900C5A···Zniii4.148 (4)
Br1···H3Bii3.0700C5A···C6Avii3.425 (6)
Br1···H1Bi2.7000C5B···C5Bix3.472 (6)
Br2···H2Aiv3.0900C6A···C4Avii3.387 (6)
Br2···H3Aiv2.9100C6A···C5Avii3.425 (6)
Br2···H6Bi3.2000C6A···O2Bvii3.292 (6)
Br2···H2B2.6500C6B···O2Bv3.387 (6)
Br2···H3Aiii3.2200C6B···C2Bv3.588 (6)
Br2···H5Aiii2.8700C6B···Br2viii3.404 (5)
Zn···C5Aiii4.148 (4)C2A···H1Avi2.8500
Zn···H2A2.9100C5B···H5Bix3.0400
Zn···H2B2.8800H1A···O2Avi1.9400
Zn···H5Aiii3.6300H1A···C2Avi2.8500
O2A···Br23.488 (3)H1B···Br1viii2.7000
O2A···N3B2.915 (5)H2A···Br12.7400
O2A···C4B3.116 (5)H2A···Br2ii3.0900
O2A···N1Avi2.766 (5)H2A···Zn2.9100
O2B···C6Bv3.387 (6)H2B···Br1iv3.1900
O2B···Br13.558 (2)H2B···Br22.6500
O2B···N3A3.257 (5)H2B···Zn2.8800
O2B···N4Bii3.003 (5)H3A···Br2ii2.9100
O2B···C6Avii3.292 (6)H3A···H5A2.4000
O2A···H1Avi1.9400H3A···Br2iii3.2200
O2B···H5Bii2.8600H3B···Br1iv3.0700
O2B···H3Bii2.1900H3B···O2Biv2.1900
O2B···H6Avii2.4200H3B···H5B2.3800
N1A···O2Avi2.766 (5)H5A···H3A2.4000
N1A···C5Avii3.357 (5)H5A···Br2iii2.8700
N1B···Br1viii3.483 (3)H5A···Zniii3.6300
N1B···C2Bv3.306 (5)H5B···O2Biv2.8600
N3A···Br23.511 (3)H5B···H3B2.3800
N3A···O2B3.257 (5)H5B···C5Bix3.0400
N3A···N3B3.295 (5)H6A···O2Bvii2.4200
N3B···O2A2.915 (5)H6B···Br2viii3.2000
N3B···N3A3.295 (5)H6B···Br1v3.1100
N4A···Br13.577 (4)
Br1—Zn—Br2104.31 (2)O2A—C2A—N1A121.3 (4)
Br1—Zn—N3A116.18 (9)N1A—C2A—N3A118.6 (4)
Br1—Zn—N3B111.56 (10)O2A—C2A—N3A120.2 (4)
Br2—Zn—N3A102.82 (9)O2B—C2B—N3B121.7 (3)
Br2—Zn—N3B115.31 (9)O2B—C2B—N1B120.6 (4)
N3A—Zn—N3B106.66 (13)N1B—C2B—N3B117.7 (4)
C2A—N1A—C6A122.6 (4)N3A—C4A—C5A121.7 (4)
C2B—N1B—C6B122.4 (4)N3A—C4A—N4A117.7 (4)
Zn—N3A—C2A109.0 (3)N4A—C4A—C5A120.6 (4)
Zn—N3A—C4A132.0 (3)N4B—C4B—C5B119.5 (4)
C2A—N3A—C4A119.0 (4)N3B—C4B—C5B121.7 (4)
Zn—N3B—C2B109.3 (2)N3B—C4B—N4B118.8 (4)
Zn—N3B—C4B128.1 (3)C4A—C5A—C6A117.9 (4)
C2B—N3B—C4B119.9 (3)C4B—C5B—C6B117.8 (4)
C2A—N1A—H1A119.00N1A—C6A—C5A120.2 (4)
C6A—N1A—H1A119.00N1B—C6B—C5B120.4 (4)
C2B—N1B—H1B119.00C4A—C5A—H5A121.00
C6B—N1B—H1B119.00C6A—C5A—H5A121.00
H2A—N4A—H3A120.00C4B—C5B—H5B121.00
C4A—N4A—H2A120.00C6B—C5B—H5B121.00
C4A—N4A—H3A120.00N1A—C6A—H6A120.00
H2B—N4B—H3B120.00C5A—C6A—H6A120.00
C4B—N4B—H2B120.00N1B—C6B—H6B120.00
C4B—N4B—H3B120.00C5B—C6B—H6B120.00
Br1—Zn—N3A—C2A−176.9 (2)C4A—N3A—C2A—O2A−179.1 (4)
Br1—Zn—N3A—C4A5.3 (4)C4A—N3A—C2A—N1A2.1 (6)
Br2—Zn—N3A—C2A69.9 (3)Zn—N3A—C4A—N4A−5.4 (6)
Br2—Zn—N3A—C4A−107.9 (4)Zn—N3A—C4A—C5A175.1 (3)
N3B—Zn—N3A—C2A−51.9 (3)C2A—N3A—C4A—N4A177.1 (4)
N3B—Zn—N3A—C4A130.4 (4)C2A—N3A—C4A—C5A−2.5 (6)
Br1—Zn—N3B—C2B70.0 (3)Zn—N3B—C2B—O2B−13.9 (5)
Br1—Zn—N3B—C4B−128.9 (3)Zn—N3B—C2B—N1B166.2 (3)
Br2—Zn—N3B—C2B−171.3 (2)C4B—N3B—C2B—O2B−176.7 (4)
Br2—Zn—N3B—C4B−10.2 (4)C4B—N3B—C2B—N1B3.3 (5)
N3A—Zn—N3B—C2B−57.8 (3)Zn—N3B—C4B—N4B20.3 (5)
N3A—Zn—N3B—C4B103.2 (3)Zn—N3B—C4B—C5B−160.4 (3)
C6A—N1A—C2A—O2A−179.2 (4)C2B—N3B—C4B—N4B179.6 (4)
C6A—N1A—C2A—N3A−0.4 (6)C2B—N3B—C4B—C5B−1.1 (6)
C2A—N1A—C6A—C5A−1.0 (6)N3A—C4A—C5A—C6A1.2 (6)
C6B—N1B—C2B—O2B175.8 (4)N4A—C4A—C5A—C6A−178.4 (4)
C6B—N1B—C2B—N3B−4.2 (6)N3B—C4B—C5B—C6B−0.4 (6)
C2B—N1B—C6B—C5B2.8 (7)N4B—C4B—C5B—C6B178.9 (4)
Zn—N3A—C2A—O2A2.8 (5)C4A—C5A—C6A—N1A0.6 (6)
Zn—N3A—C2A—N1A−176.0 (3)C4B—C5B—C6B—N1B−0.4 (7)

Symmetry codes: (i) x, y+1, z; (ii) x−1, y, z; (iii) −x+1, −y+2, −z+1; (iv) x+1, y, z; (v) −x+1, −y+1, −z+2; (vi) −x+2, −y+1, −z+1; (vii) −x+1, −y+1, −z+1; (viii) x, y−1, z; (ix) −x+2, −y+1, −z+2.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1A—H1A···O2Avi0.861.942.766 (5)161
N1B—H1B···Br1viii0.862.703.483 (3)151
N4A—H2A···Br10.862.743.577 (4)165
N4B—H2B···Br20.862.653.454 (3)155
N4A—H3A···Br2ii0.862.913.339 (4)112
N4B—H3B···O2Biv0.862.193.003 (5)157
C5A—H5A···Br2iii0.932.873.726 (4)153
C6A—H6A···O2Bvii0.932.423.292 (6)156

Symmetry codes: (vi) −x+2, −y+1, −z+1; (viii) x, y−1, z; (ii) x−1, y, z; (iv) x+1, y, z; (iii) −x+1, −y+2, −z+1; (vii) −x+1, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HG2756).

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