organic compounds
Cytosinium hydrogen selenite
aLaboratoire des Structures, Propriétés et Interactions InterAtomiques, Université Abbes Laghrour-Khenchela, 40000 Khenchela, Algeria
*Correspondence e-mail: benalicherif@hotmail.com
In the 4H6N3O+·HSeO3−, 6-amino-2-methylidene-2,3-dihydropyrimidin-1-ium hydrogen selenite, the hydrogenselenite anions and the cytosinium cations are linked via N—H⋯O, N—H⋯Se, O—H⋯O, O—H··Se and C—H⋯O hydrogen bonds, forming a three-dimensional framework.
of the title salt, CCCDC reference: 982125
Related literature
For the ), and of cytosine monohydrate, see: Jeffrey & Kinoshita (1963). For examples of some inorganic cytosinium salts, see: Mandel (1977); Bagieu-Beucher (1990). For examples of the structures of cytosinium salts of organic acids, see: Gdaniec et al. (1989); Smith et al. (2005). For examples of the structure of the hydrogenselenite anion, see: Richie & Harrison (2003); Wang et al. (2006); Chomnilpan et al. (1981).
of cytosine, see: Barker & Marsh (1964Experimental
Crystal data
|
Refinement
Data collection: COLLECT (Hooft, 1998); cell DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2013 and PLATON.
Supporting information
CCDC reference: 982125
10.1107/S1600536814001275/su2689sup1.cif
contains datablocks Global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814001275/su2689Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814001275/su2689Isup3.cml
Selenious acid (H2SeO3) was added to an aqueous solution of cytosine in the stoichiometric ratio 1:1, at room temperature. After four weeks colourless prismatic crystals of the title salt were obtained.
All the H atoms could be located in difference Fourier maps and this was confirmed by plotting difference Fourier maps using the ContourDif routine in PLATON (Spek, 2009). In the final cycles of
the NH2 distances were restrained to N-H = 0.86 (2) and H···H = 1.33 (2) Å with Uiso(H) = 1.2Ueq(N). The OH distance was restrained to O-H = 0.82 (2) Å with Uiso(H) = 1.5Ueq(O). The C bound H atoms were included in calculated positions and treated as riding atoms: C-H = 0.93 Å with Uiso(H) = 1.2Ueq(C).The
of cytosine (Barker & Marsh, 1964) and cytosine monohydrate (Jeffrey & Kinoshita, 1963) were determined many years ago. Many inorganic cytosinium salts have been synthesized, including the hydrochloride (Mandel, 1977) and the dihydrogenmonophosphate (Bagieu-Beucher, 1990) salts. Cytosinium salts of organic acids are also common, these include for example, cytosinium trichloroacetate (Gdaniec et al., 1989) and cytosinium 3,5-dinitrosalicylate (Smith et al., 2005). We report herein on the molecular structure of a new cytosinium salt formed by the reaction of cytosine with selenious acid.The structure of the title salt is illustrated in Fig. 1. The HSeO3- ion is pyramidal with two short Se—O bonds, Se1—O3 = 1.634 (8) A° and Se1—O4 = 1.686 (6) A°, and a longer Se—OH bond, Se1—O2 = 1.738 (7) A°. These values are very similar to those described in the literature (Richie & Harrison, 2003; Wang et al., 2006; Chomnilpan et al., 1981). The geometry of this inorganic moiety clearly implies that one proton was transferred from selenious acid to cytosine.
In the crystal, the anions and cations are linked via N—H···O/Se, O-H···O/Se and C-H···O hydrogen bonds forming a three-dimensional framework (Table 1 and Fig. 2).
For the
of cytosine, see: Barker & Marsh (1964), and of cytosine monohydrate, see: Jeffrey & Kinoshita (1963). For examples of some inorganic cytosinium salts, see: Mandel (1977); Bagieu-Beucher (1990). For examples of the structures of cytosinium salts of organic acids, see: Gdaniec et al. (1989); Smith et al. (2005). For examples of the structure of the hydrogenselenite anion, see: Richie & Harrison (2003); Wang et al. (2006); Chomnilpan et al. (1981). SCHEME SHOWS SULFATEData collection: COLLECT (Hooft, 1998); cell
DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2008) and PLATON (Spek, 2009).Fig. 1. A view of the molecular structure of the title salt, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. | |
Fig. 2. A view along the b axis of the crystal packing of the title compound. The hydrogen-bonds are shown as dashed lines (See Table 1 for details). |
C4H6N3O+·HSeO3− | Dx = 2.074 Mg m−3 |
Mr = 240.09 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, Pca21 | Cell parameters from 5415 reflections |
a = 7.0051 (3) Å | θ = 3.8–29.5° |
b = 8.6342 (2) Å | µ = 4.86 mm−1 |
c = 12.7131 (3) Å | T = 293 K |
V = 768.93 (4) Å3 | Prism, colourless |
Z = 4 | 0.20 × 0.15 × 0.10 mm |
F(000) = 472 |
Nonius KappaCCD diffractometer | 1494 independent reflections |
Radiation source: fine-focus sealed tube | 1283 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.067 |
ω – θ scans | θmax = 26.0°, θmin = 3.8° |
Absorption correction: multi-scan (Blessing, 1995) | h = −8→8 |
Tmin = 0.295, Tmax = 0.369 | k = −10→10 |
4568 measured reflections | l = −14→15 |
Refinement on F2 | Hydrogen site location: difference Fourier map |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.042 | w = 1/[σ2(Fo2) + (0.0404P)2 + 0.8215P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.098 | (Δ/σ)max < 0.001 |
S = 1.04 | Δρmax = 0.46 e Å−3 |
1494 reflections | Δρmin = −0.49 e Å−3 |
125 parameters | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
7 restraints | Extinction coefficient: 0.018 (4) |
Primary atom site location: structure-invariant direct methods | Absolute structure: Flack parameter determined using 518 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
Secondary atom site location: difference Fourier map | Absolute structure parameter: −0.02 (3) |
C4H6N3O+·HSeO3− | V = 768.93 (4) Å3 |
Mr = 240.09 | Z = 4 |
Orthorhombic, Pca21 | Mo Kα radiation |
a = 7.0051 (3) Å | µ = 4.86 mm−1 |
b = 8.6342 (2) Å | T = 293 K |
c = 12.7131 (3) Å | 0.20 × 0.15 × 0.10 mm |
Nonius KappaCCD diffractometer | 1494 independent reflections |
Absorption correction: multi-scan (Blessing, 1995) | 1283 reflections with I > 2σ(I) |
Tmin = 0.295, Tmax = 0.369 | Rint = 0.067 |
4568 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.098 | Δρmax = 0.46 e Å−3 |
S = 1.04 | Δρmin = −0.49 e Å−3 |
1494 reflections | Absolute structure: Flack parameter determined using 518 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013) |
125 parameters | Absolute structure parameter: −0.02 (3) |
7 restraints |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.9370 (10) | 0.0316 (8) | 0.0502 (5) | 0.050 (2) | |
N1 | 0.8269 (12) | −0.0384 (8) | 0.2127 (7) | 0.0392 (19) | |
H1A | 0.832 (17) | −0.134 (5) | 0.194 (8) | 0.047* | |
N2 | 0.8534 (12) | 0.2200 (8) | 0.1669 (6) | 0.0363 (17) | |
H2A | 0.885 (14) | 0.300 (8) | 0.130 (7) | 0.044* | |
N3 | 0.7775 (19) | 0.4148 (8) | 0.2818 (10) | 0.047 (3) | |
H3A | 0.732 (17) | 0.455 (9) | 0.337 (5) | 0.056* | |
H3B | 0.817 (16) | 0.489 (8) | 0.245 (6) | 0.056* | |
C1 | 0.8779 (14) | 0.0666 (10) | 0.1365 (8) | 0.037 (2) | |
C2 | 0.7901 (14) | 0.2661 (10) | 0.2619 (8) | 0.036 (2) | |
C3 | 0.7485 (14) | 0.1527 (10) | 0.3383 (8) | 0.041 (2) | |
H3 | 0.7088 | 0.1799 | 0.4056 | 0.049* | |
C4 | 0.7686 (17) | 0.0029 (10) | 0.3095 (8) | 0.041 (2) | |
H4 | 0.7413 | −0.0742 | 0.3583 | 0.049* | |
Se1 | 0.43127 (11) | 0.36795 (7) | 0.02452 (11) | 0.0378 (4) | |
O2 | 0.2460 (11) | 0.3114 (7) | −0.0579 (6) | 0.0444 (16) | |
H2 | 0.147 (10) | 0.350 (12) | −0.038 (10) | 0.067* | |
O3 | 0.3461 (15) | 0.3439 (7) | 0.1431 (6) | 0.054 (2) | |
O4 | 0.4180 (9) | 0.5615 (6) | 0.0084 (8) | 0.0432 (19) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.063 (4) | 0.039 (3) | 0.048 (6) | 0.004 (3) | 0.007 (3) | −0.006 (3) |
N1 | 0.051 (5) | 0.022 (3) | 0.045 (5) | 0.001 (3) | −0.005 (4) | 0.003 (3) |
N2 | 0.051 (4) | 0.023 (4) | 0.035 (4) | 0.000 (3) | −0.001 (3) | 0.004 (3) |
N3 | 0.062 (8) | 0.029 (3) | 0.049 (5) | 0.002 (5) | 0.004 (5) | −0.004 (4) |
C1 | 0.038 (5) | 0.024 (4) | 0.047 (6) | −0.001 (4) | −0.004 (4) | −0.004 (4) |
C2 | 0.043 (7) | 0.030 (4) | 0.035 (6) | 0.004 (4) | −0.002 (5) | −0.001 (4) |
C3 | 0.050 (6) | 0.036 (5) | 0.036 (5) | −0.004 (4) | 0.000 (4) | −0.002 (4) |
C4 | 0.045 (6) | 0.035 (5) | 0.042 (6) | −0.003 (4) | −0.003 (5) | 0.009 (4) |
Se1 | 0.0425 (5) | 0.0233 (4) | 0.0475 (5) | 0.0031 (3) | −0.0018 (7) | −0.0008 (7) |
O2 | 0.046 (4) | 0.035 (3) | 0.053 (4) | 0.002 (3) | −0.002 (3) | −0.009 (3) |
O3 | 0.098 (6) | 0.022 (3) | 0.041 (4) | 0.005 (3) | −0.001 (4) | 0.002 (3) |
O4 | 0.052 (3) | 0.023 (3) | 0.055 (5) | −0.001 (2) | 0.003 (4) | −0.001 (3) |
O1—C1 | 1.211 (11) | N3—H3B | 0.84 (3) |
N1—C4 | 1.345 (14) | C2—C3 | 1.409 (13) |
N1—C1 | 1.374 (13) | C3—C4 | 1.352 (12) |
N1—H1A | 0.85 (3) | C3—H3 | 0.9300 |
N2—C2 | 1.346 (11) | C4—H4 | 0.9300 |
N2—C1 | 1.391 (11) | Se1—O3 | 1.634 (8) |
N2—H2A | 0.86 (3) | Se1—O4 | 1.686 (6) |
N3—C2 | 1.312 (12) | Se1—O2 | 1.738 (7) |
N3—H3A | 0.84 (3) | O2—H2 | 0.81 (3) |
C4—N1—C1 | 123.3 (7) | N3—C2—C3 | 122.2 (10) |
C4—N1—H1A | 121 (7) | N2—C2—C3 | 118.7 (8) |
C1—N1—H1A | 115 (7) | C4—C3—C2 | 117.2 (9) |
C2—N2—C1 | 124.9 (8) | C4—C3—H3 | 121.4 |
C2—N2—H2A | 110 (7) | C2—C3—H3 | 121.4 |
C1—N2—H2A | 125 (7) | N1—C4—C3 | 122.2 (8) |
C2—N3—H3A | 126 (6) | N1—C4—H4 | 118.9 |
C2—N3—H3B | 128 (6) | C3—C4—H4 | 118.9 |
H3A—N3—H3B | 106 (5) | O3—Se1—O4 | 102.6 (4) |
O1—C1—N1 | 124.3 (9) | O3—Se1—O2 | 104.3 (5) |
O1—C1—N2 | 122.1 (9) | O4—Se1—O2 | 99.4 (4) |
N1—C1—N2 | 113.6 (8) | Se1—O2—H2 | 110 (9) |
N3—C2—N2 | 119.0 (9) | ||
C4—N1—C1—O1 | 177.3 (10) | C1—N2—C2—C3 | 1.5 (15) |
C4—N1—C1—N2 | −3.4 (14) | N3—C2—C3—C4 | −179.2 (12) |
C2—N2—C1—O1 | −179.4 (10) | N2—C2—C3—C4 | −2.4 (15) |
C2—N2—C1—N1 | 1.3 (13) | C1—N1—C4—C3 | 2.7 (17) |
C1—N2—C2—N3 | 178.4 (10) | C2—C3—C4—N1 | 0.4 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···Se1i | 0.85 (3) | 3.04 (6) | 3.789 (9) | 148 (9) |
N1—H1A···O3i | 0.85 (3) | 1.93 (3) | 2.785 (10) | 176 (10) |
N2—H2A···O4ii | 0.86 (3) | 1.97 (5) | 2.798 (12) | 160 (10) |
N3—H3A···Se1iii | 0.84 (3) | 3.06 (3) | 3.896 (12) | 174 (7) |
N3—H3A···O2iii | 0.84 (3) | 2.42 (7) | 3.126 (12) | 141 (8) |
N3—H3A···O4iii | 0.84 (3) | 2.42 (4) | 3.196 (17) | 152 (8) |
N3—H3B···O3ii | 0.84 (3) | 1.95 (4) | 2.772 (12) | 166 (12) |
O2—H2···Se1iv | 0.81 (3) | 2.97 (6) | 3.691 (7) | 149 (10) |
O2—H2···O4iv | 0.81 (3) | 1.87 (3) | 2.682 (10) | 180 (14) |
C3—H3···O1v | 0.93 | 2.46 | 3.168 (12) | 133 |
C4—H4···O2vi | 0.93 | 2.31 | 3.196 (11) | 159 |
Symmetry codes: (i) x+1/2, −y, z; (ii) x+1/2, −y+1, z; (iii) −x+1, −y+1, z+1/2; (iv) x−1/2, −y+1, z; (v) −x+3/2, y, z+1/2; (vi) −x+1, −y, z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···Se1i | 0.85 (3) | 3.04 (6) | 3.789 (9) | 148 (9) |
N1—H1A···O3i | 0.85 (3) | 1.93 (3) | 2.785 (10) | 176 (10) |
N2—H2A···O4ii | 0.86 (3) | 1.97 (5) | 2.798 (12) | 160 (10) |
N3—H3A···Se1iii | 0.84 (3) | 3.06 (3) | 3.896 (12) | 174 (7) |
N3—H3A···O2iii | 0.84 (3) | 2.42 (7) | 3.126 (12) | 141 (8) |
N3—H3A···O4iii | 0.84 (3) | 2.42 (4) | 3.196 (17) | 152 (8) |
N3—H3B···O3ii | 0.84 (3) | 1.95 (4) | 2.772 (12) | 166 (12) |
O2—H2···Se1iv | 0.81 (3) | 2.97 (6) | 3.691 (7) | 149 (10) |
O2—H2···O4iv | 0.81 (3) | 1.87 (3) | 2.682 (10) | 180 (14) |
C3—H3···O1v | 0.93 | 2.46 | 3.168 (12) | 133 |
C4—H4···O2vi | 0.93 | 2.31 | 3.196 (11) | 159 |
Symmetry codes: (i) x+1/2, −y, z; (ii) x+1/2, −y+1, z; (iii) −x+1, −y+1, z+1/2; (iv) x−1/2, −y+1, z; (v) −x+3/2, y, z+1/2; (vi) −x+1, −y, z+1/2. |
Acknowledgements
We are grateful to Dr M. Giorgi, Faculté des Sciences et Techniques de Saint Jeŕome, Marseille, France, for providing access to the X-ray diffraction facilities. We also thank Abbes Laghrour Khenchela University, le Ministére de l'Enseignement Supérieur et de la Recherche Scientifique–Algeria and the Direction Générale de la Recherche Scientifique et du Développement Technologique–Algeria for financial support.
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The crystal structure of cytosine (Barker & Marsh, 1964) and cytosine monohydrate (Jeffrey & Kinoshita, 1963) were determined many years ago. Many inorganic cytosinium salts have been synthesized, including the hydrochloride (Mandel, 1977) and the dihydrogenmonophosphate (Bagieu-Beucher, 1990) salts. Cytosinium salts of organic acids are also common, these include for example, cytosinium trichloroacetate (Gdaniec et al., 1989) and cytosinium 3,5-dinitrosalicylate (Smith et al., 2005). We report herein on the molecular structure of a new cytosinium salt formed by the reaction of cytosine with selenious acid.
The structure of the title salt is illustrated in Fig. 1. The HSeO3- ion is pyramidal with two short Se—O bonds, Se1—O3 = 1.634 (8) A° and Se1—O4 = 1.686 (6) A°, and a longer Se—OH bond, Se1—O2 = 1.738 (7) A°. These values are very similar to those described in the literature (Richie & Harrison, 2003; Wang et al., 2006; Chomnilpan et al., 1981). The geometry of this inorganic moiety clearly implies that one proton was transferred from selenious acid to cytosine.
In the crystal, the anions and cations are linked via N—H···O/Se, O-H···O/Se and C-H···O hydrogen bonds forming a three-dimensional framework (Table 1 and Fig. 2).