Literature DB >> 21577678

Adeninium cytosinium sulfate.

Aouatef Cherouana, Raja Bousboua, Lamia Bendjeddou, Slimane Dahaoui, Claude Lecomte.   

Abstract

In the title compound, C(5)H(6)N(5) (+)·C(4)H(6)N(3)O(+)·SO(4) (2-), the adeninium (AdH(+)) and cytosinium (CytH(+)) cations and sulfate dianion are involved in a three-dimensional hydrogen-bonding network with four different modes, viz. AdH(+)⋯AdH(+), AdH(+)⋯CytH(+), AdH(+)⋯SO(4) (2-) and CytH(+)⋯SO(4) (2-). The adeninium cations form N-H⋯N dimers through the Hoogsteen faces, generating a characteristic R(2) (2)(10) motif. This AdH(+)⋯AdH(+) hydrogen bond in combination with AdH(+)⋯CytH(+ )H-bonds leads to two-dimensional cationic ribbons parallel to the a axis. The sulfate anions inter-link the ribbons into a three-dimensional hydrogen-bonding network and thus reinforce the crystal structure.

Entities:  

Year:  2009        PMID: 21577678      PMCID: PMC2969916          DOI: 10.1107/S1600536809034023

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


Related literature

Nucleobases possess multiple hydrogen-bonding sites (Saenger, 1984 ▶) and so can form an abundance of aggregates through hydrogen bonds, from dimers to infinite extended species, see: Jai-nhuknan et al. (1997 ▶); Bendjeddou et al. (2003 ▶); Smith et al. (2005 ▶); Sridhar & Ravikumar (2007 ▶). For protonated nucleobases in acid-base catalysis, see: Lippert (2005 ▶). For their use in the construction of highly ordered supra­molecular nanostructures which are of inter­est for their potential applications as mol­ecular devices, see: Lehn (1995 ▶); Gottarelli et al. (2000 ▶). Bond lengths in adeninium cations are dependent on the degree of protonation, see: Hingerty et al. (1981 ▶); Langer & Huml (1978 ▶). For bond angles in neutral adenine, see: Voet & Rich (1970 ▶). For related structures with a cytosinium cation, see: Prabakaran et al. (2001 ▶); Smith et al. (2005 ▶); Sridhar & Ravikumar (2008 ▶). For graph-set motifs, see: Bernstein et al. (1995 ▶). For hydrogen bond ing, see: Jeffrey & Saenger (1991 ▶). For pKa values for cytosine, see: Stecher (1968 ▶).

Experimental

Crystal data

C5H6N5 +·C4H6N3O+·SO4 2− M = 344.33 Monoclinic, a = 9.180 (2) Å b = 12.948 (3) Å c = 11.328 (3) Å β = 99.356 (2)° V = 1328.6 (5) Å3 Z = 4 Mo Kα radiation μ = 0.29 mm−1 T = 100 K 0.39 × 0.26 × 0.12 mm

Data collection

Oxford Diffraction Xcalibur Saphire2 CCD diffractometer Absorption correction: analytical (CrysAlis RED; Oxford Diffraction, 2008 ▶) T min = 0.921, T max = 0.975 57856 measured reflections 5843 independent reflections 5061 reflections with I > 2σ(I) R int = 0.026

Refinement

R[F 2 > 2σ(F 2)] = 0.027 wR(F 2) = 0.088 S = 1.04 5843 reflections 232 parameters 8 restraints H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.51 e Å−3 Δρmin = −0.51 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2008 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2008 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SIR92 (Altomare et al., 1993 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶) and Mercury (Macrae et al., 2006 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809034023/at2867sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809034023/at2867Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H6N5+·C4H6N3O+·SO42F(000) = 712
Mr = 344.33Dx = 1.721 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 57856 reflections
a = 9.180 (2) Åθ = 3.1–35.0°
b = 12.948 (3) ŵ = 0.29 mm1
c = 11.328 (3) ÅT = 100 K
β = 99.356 (2)°Prism, colourless
V = 1328.6 (5) Å30.39 × 0.26 × 0.12 mm
Z = 4
Oxford Diffraction Xcalibur Saphire2 CCD diffractometer5843 independent reflections
Radiation source: fine-focus sealed tube5061 reflections with I > 2σ(I)
graphiteRint = 0.026
φ and ω scansθmax = 35.0°, θmin = 3.1°
Absorption correction: analytical (CrysAlis RED; Oxford Diffraction, 2008)h = −14→14
Tmin = 0.921, Tmax = 0.975k = −20→20
57856 measured reflectionsl = −17→18
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.027Hydrogen site location: difference Fourier map
wR(F2) = 0.088H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0602P)2 + 0.1819P] where P = (Fo2 + 2Fc2)/3
5843 reflections(Δ/σ)max = 0.001
232 parametersΔρmax = 0.51 e Å3
8 restraintsΔρmin = −0.51 e Å3
Experimental. CrysAlis RED (Oxford Diffraction, 2008) Analytical numeric absorption correction using a multifaceted crystal model based on expressions derived by R.C. Clark & J.S. Reid.
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 of F^2^ against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The threshold expression of F^2^ > σ(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.
xyzUiso*/Ueq
N1A0.89503 (7)0.08114 (5)0.15030 (6)0.0102 (1)
N2A0.93054 (8)−0.04224 (5)0.30191 (6)0.0114 (2)
N3A0.92695 (7)0.26232 (5)0.17622 (6)0.0113 (2)
N7A1.01108 (7)0.14551 (5)0.46688 (6)0.0097 (1)
N9A1.00189 (7)0.30483 (5)0.38697 (6)0.0106 (2)
C2A0.89521 (8)0.18034 (6)0.10957 (7)0.0113 (2)
C4A0.96300 (8)0.23844 (5)0.29397 (6)0.0091 (2)
C5A0.96826 (7)0.14027 (5)0.34460 (6)0.0083 (2)
C6A0.93243 (7)0.05505 (5)0.26787 (6)0.0087 (1)
C8A1.02951 (8)0.24570 (5)0.48772 (7)0.0106 (2)
O5C0.58498 (6)0.24982 (4)0.27802 (5)0.0133 (2)
N1C0.59982 (7)0.08175 (5)0.33878 (6)0.0100 (1)
N2C0.76585 (7)0.18374 (5)0.67114 (6)0.0107 (2)
N3C0.67261 (7)0.21469 (5)0.47342 (6)0.0092 (1)
C2C0.61681 (8)0.18570 (5)0.35794 (7)0.0093 (2)
C4C0.71397 (7)0.14707 (5)0.56532 (7)0.0085 (2)
C5C0.69956 (8)0.03932 (5)0.54009 (7)0.0100 (2)
C6C0.64100 (8)0.01083 (5)0.42725 (7)0.0102 (2)
S10.27538 (2)0.03329 (1)0.11795 (2)0.0083 (1)
O10.19268 (7)−0.06314 (4)0.12530 (5)0.0137 (2)
O20.24941 (6)0.10652 (4)0.21156 (5)0.0119 (1)
O30.43624 (6)0.01038 (4)0.13141 (5)0.0122 (1)
O40.22552 (6)0.07936 (4)−0.00242 (5)0.0115 (1)
H1A0.8721 (13)0.0315 (8)0.0979 (9)0.0123*
H2A0.870690.190490.027470.0135*
H3A0.9548 (13)−0.0569 (10)0.3778 (8)0.0136*
H4A0.9167 (13)−0.0894 (8)0.2481 (9)0.0136*
H8A1.058530.273100.563800.0127*
H9A1.0154 (13)0.3714 (6)0.3849 (11)0.0127*
H1C0.5516 (12)0.0640 (9)0.2698 (8)0.0120*
H2C0.7866 (13)0.1437 (9)0.7326 (9)0.0129*
H3C0.6899 (12)0.2814 (6)0.4829 (10)0.0111*
H4C0.7671 (12)0.2495 (6)0.6843 (10)0.0129*
H5C0.72934−0.009720.599070.0120*
H6C0.62847−0.059050.409480.0122*
U11U22U33U12U13U23
N1A0.0133 (2)0.0090 (2)0.0078 (3)−0.0006 (2)−0.0001 (2)−0.0007 (2)
N2A0.0175 (3)0.0066 (2)0.0096 (3)−0.0002 (2)0.0010 (2)−0.0009 (2)
N3A0.0146 (3)0.0097 (2)0.0088 (3)−0.0012 (2)−0.0001 (2)0.0010 (2)
N7A0.0122 (2)0.0085 (2)0.0080 (3)−0.0007 (2)0.0007 (2)−0.0006 (2)
N9A0.0145 (3)0.0070 (2)0.0098 (3)−0.0019 (2)0.0008 (2)−0.0005 (2)
C2A0.0141 (3)0.0104 (3)0.0087 (3)−0.0007 (2)−0.0002 (2)0.0012 (2)
C4A0.0107 (3)0.0076 (3)0.0089 (3)−0.0010 (2)0.0009 (2)−0.0001 (2)
C5A0.0101 (3)0.0070 (2)0.0077 (3)−0.0005 (2)0.0010 (2)−0.0002 (2)
C6A0.0097 (2)0.0080 (2)0.0082 (3)0.0002 (2)0.0010 (2)−0.0002 (2)
C8A0.0133 (3)0.0093 (3)0.0089 (3)−0.0015 (2)0.0006 (2)−0.0006 (2)
O5C0.0198 (3)0.0095 (2)0.0093 (3)0.0003 (2)−0.0017 (2)0.0021 (2)
N1C0.0126 (2)0.0077 (2)0.0088 (3)−0.0007 (2)−0.0013 (2)−0.0008 (2)
N2C0.0144 (3)0.0091 (2)0.0079 (3)−0.0005 (2)−0.0006 (2)0.0002 (2)
N3C0.0127 (2)0.0064 (2)0.0078 (3)−0.0001 (2)−0.0007 (2)0.0001 (2)
C2C0.0103 (3)0.0081 (3)0.0089 (3)−0.0001 (2)0.0002 (2)−0.0002 (2)
C4C0.0089 (2)0.0082 (3)0.0084 (3)0.0000 (2)0.0011 (2)0.0009 (2)
C5C0.0116 (3)0.0072 (3)0.0106 (3)−0.0002 (2)0.0004 (2)0.0009 (2)
C6C0.0113 (3)0.0075 (3)0.0116 (3)−0.0007 (2)0.0013 (2)0.0003 (2)
S10.0115 (1)0.0059 (1)0.0067 (1)0.0002 (1)−0.0008 (1)0.0003 (1)
O10.0199 (3)0.0090 (2)0.0111 (3)−0.0048 (2)−0.0008 (2)0.0018 (2)
O20.0167 (2)0.0094 (2)0.0097 (3)0.0013 (2)0.0025 (2)−0.0014 (2)
O30.0123 (2)0.0111 (2)0.0122 (3)0.0025 (2)−0.0013 (2)−0.0024 (2)
O40.0174 (2)0.0083 (2)0.0076 (2)0.0005 (2)−0.0016 (2)0.0019 (2)
S1—O11.4706 (10)N1C—C6C1.3665 (12)
S1—O21.4706 (10)N1C—C2C1.3682 (12)
S1—O31.4895 (10)N2C—C4C1.3052 (12)
S1—O41.4905 (10)N3C—C4C1.3660 (12)
O5C—C2C1.2281 (11)N3C—C2C1.3772 (13)
N1A—C2A1.3649 (13)N1C—H1C0.864 (9)
N1A—C6A1.3628 (12)N2C—H4C0.864 (8)
N2A—C6A1.3184 (12)N2C—H2C0.864 (11)
N3A—C2A1.3077 (12)N3C—H3C0.882 (8)
N3A—C4A1.3568 (12)C4A—C5A1.3921 (12)
N7A—C8A1.3245 (12)C5A—C6A1.4101 (12)
N7A—C5A1.3787 (12)C2A—H2A0.9300
N9A—C4A1.3616 (12)C8A—H8A0.9300
N9A—C8A1.3634 (12)C4C—C5C1.4260 (12)
N1A—H1A0.877 (10)C5C—C6C1.3548 (13)
N2A—H4A0.858 (10)C5C—H5C0.9300
N2A—H3A0.873 (9)C6C—H6C0.9300
N9A—H9A0.872 (8)
O1—S1—O4107.88 (3)N3A—C4A—C5A126.85 (6)
O1—S1—O2111.16 (3)N3A—C4A—N9A127.46 (6)
O1—S1—O3109.72 (3)N9A—C4A—C5A105.70 (6)
O3—S1—O4108.98 (3)N7A—C5A—C4A110.74 (6)
O2—S1—O3109.20 (3)N7A—C5A—C6A131.12 (6)
O2—S1—O4109.87 (3)C4A—C5A—C6A118.14 (6)
C2A—N1A—C6A123.35 (6)N1A—C6A—N2A120.63 (6)
C2A—N3A—C4A112.24 (6)N2A—C6A—C5A125.47 (6)
C5A—N7A—C8A103.57 (6)N1A—C6A—C5A113.89 (6)
C4A—N9A—C8A106.43 (6)N7A—C8A—N9A113.57 (7)
C2A—N1A—H1A118.3 (7)N3A—C2A—H2A117.00
C6A—N1A—H1A118.3 (7)N1A—C2A—H2A117.00
H3A—N2A—H4A122.0 (11)N7A—C8A—H8A123.00
C6A—N2A—H3A118.8 (8)N9A—C8A—H8A123.00
C6A—N2A—H4A118.7 (7)O5C—C2C—N3C121.54 (6)
C4A—N9A—H9A128.6 (8)O5C—C2C—N1C122.74 (7)
C8A—N9A—H9A124.7 (8)N1C—C2C—N3C115.72 (6)
C2C—N1C—C6C122.27 (7)N2C—C4C—N3C118.78 (6)
C2C—N3C—C4C124.30 (6)N2C—C4C—C5C123.24 (7)
C6C—N1C—H1C121.6 (8)N3C—C4C—C5C117.98 (7)
C2C—N1C—H1C115.7 (8)C4C—C5C—C6C117.72 (7)
C4C—N2C—H2C121.4 (7)N1C—C6C—C5C121.94 (6)
H2C—N2C—H4C117.2 (10)C4C—C5C—H5C121.00
C4C—N2C—H4C120.6 (7)C6C—C5C—H5C121.00
C2C—N3C—H3C114.5 (7)C5C—C6C—H6C119.00
C4C—N3C—H3C120.9 (7)N1C—C6C—H6C119.00
N1A—C2A—N3A125.53 (7)
D—H···AD—HH···AD···AD—H···A
N1A—H1A···O1i0.877 (10)2.535 (10)3.1036 (19)123.3 (8)
N1A—H1A···O4i0.877 (10)1.928 (11)2.7833 (17)164.5 (11)
N1C—H1C···O30.864 (9)1.877 (10)2.7350 (17)172.0 (11)
N2C—H2C···O1ii0.864 (11)1.902 (11)2.7596 (17)171.8 (11)
N2A—H3A···N7Aiii0.873 (9)2.081 (10)2.9118 (18)158.7 (12)
N3C—H3C···O4iv0.882 (8)1.835 (8)2.7164 (17)178.2 (11)
N2A—H4A···O5Cv0.858 (10)2.102 (10)2.8368 (18)143.3 (9)
N2C—H4C···O2iv0.864 (8)1.901 (8)2.7622 (17)174.4 (11)
N9A—H9A···O3vi0.872 (8)1.870 (8)2.7364 (17)172.5 (12)
C2A—H2A···O1i0.93002.39003.0553 (19)128.00
C5C—H5C···O2ii0.93002.46003.357 (2)161.00
C6C—H6C···N3Av0.93002.53003.447 (2)170.00
C8A—H8A···O5Civ0.93002.42003.245 (2)148.00
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1A—H1A⋯O1i0.877 (10)2.535 (10)3.1036 (19)123.3 (8)
N1A—H1A⋯O4i0.877 (10)1.928 (11)2.7833 (17)164.5 (11)
N1C—H1C⋯O30.864 (9)1.877 (10)2.7350 (17)172.0 (11)
N2C—H2C⋯O1ii0.864 (11)1.902 (11)2.7596 (17)171.8 (11)
N2A—H3A⋯N7Aiii0.873 (9)2.081 (10)2.9118 (18)158.7 (12)
N3C—H3C⋯O4iv0.882 (8)1.835 (8)2.7164 (17)178.2 (11)
N2A—H4A⋯O5Cv0.858 (10)2.102 (10)2.8368 (18)143.3 (9)
N2C—H4C⋯O2iv0.864 (8)1.901 (8)2.7622 (17)174.4 (11)
N9A—H9A⋯O3vi0.872 (8)1.870 (8)2.7364 (17)172.5 (12)
C2A—H2A⋯O1i0.93002.39003.0553 (19)128.00
C5C—H5C⋯O2ii0.93002.46003.357 (2)161.00
C6C—H6C⋯N3Av0.93002.53003.447 (2)170.00
C8A—H8A⋯O5Civ0.93002.42003.245 (2)148.00

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

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