Literature DB >> 21589348

Metal-nucleobase inter-action: bis[4-amino-pyrimidin-2(1H)-one-κN]dibromidozinc(II).

Ammasai Karthikeyan1, Samuel Ebenezer, Packianathan Thomas Muthiah.   

Abstract

In the title complex, [ZnBr(2)(C(4)H(5)N(3)O)(2)], the central metal ion is coordinated to two bromide ions and endocyclic N atoms of the two cytosine mol-ecules leading to a distorted tetra-hedral geometry. The structure is isotypic with [CdBr(2)(C(4)H(5)N(3)O)(2)] [Muthiah et al. (2001). Acta Cryst. E57, m558-m560]. There are two inter-ligand N-H⋯Br hydrogen bonds, generating two hydrogen-bonded rings stabilizing the coordination sphere. The complex aggregates, forming supra-molecular chains, sheets and staircases through N-H⋯O and N-H⋯Br hydrogen bonding and π-π stacking inter-actions [centroid-centroid distance = 3.616 (2) Å].

Entities:  

Year:  2010        PMID： 21589348      PMCID： PMC3011690          DOI： 10.1107/S1600536810049305

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN： 1600-5368


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 = 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 Δρmax = 0.69 e Å−3 Δρmin = −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. 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
[ZnBr2(C4H5N3O)2]Z = 2
Mr = 447.41F(000) = 432
Triclinic, P1Dx = 2.217 Mg m−3
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 mm−1
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
Bruker SMART APEXII CCD area-detector diffractometer2973 independent reflections
Radiation source: fine-focus sealed tube2204 reflections with I > 2σ(I)
graphiteRint = 0.043
φ 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 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 Å−3
0 restraintsΔρmin = −0.44 e Å−3
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.
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*
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)
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)
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
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
N1A—H1A⋯O2Ai0.861.942.766 (5)161
N1B—H1B⋯Br1ii0.862.703.483 (3)151
N4A—H2A⋯Br10.862.743.577 (4)165
N4B—H2B⋯Br20.862.653.454 (3)155
N4A—H3A⋯Br2iii0.862.913.339 (4)112
N4B—H3B⋯O2Biv0.862.193.003 (5)157
C5A—H5A⋯Br2v0.932.873.726 (4)153
C6A—H6A⋯O2Bvi0.932.423.292 (6)156

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

  3 in total

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Authors:  Jens Müller
Journal:  Metallomics       Date:  2010-03-18       Impact factor: 4.526

2.  A short history of SHELX.

Authors:  George M Sheldrick
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3.  Structure validation in chemical crystallography.

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