In the two title compounds, cytosinium hydrogen sulfate, C
4H
6N
3O
+·HSO
4−, (I), and cytosinium perchlorate, C
4H
6N
3O
+·ClO
4−, (II), the asymmetric units comprise a cytosinium cation with hydrogen sulfate and perchlorate anions, respectively. The crystal structures of (I) and (II) are similar; that of (I) is characterized by a three-dimensional N—H
O, O—H
O and C—H
O hydrogen-bonded network. In (I) and (II), two-dimensional layers are formed by N—H
O and C—H
O hydrogen bonds and, in the case of (I), they are linked by O—H
O hydrogen bonds where the anion acts as a donor and the cation as an acceptor. The hydrogen-bonded sheets in (II) form an angle of 87.1°.
Supporting information
CCDC references: 702840; 702841
The same crystallization method was used to prepare the three compounds, but in
each case the acid was different: sulfuric acid for the first, perchloric acid
for the second and nitric acid for the third. The experiment consists of
heating an equimolar solution of cytosine and mineral acid until the reaction
is complete. Colourless crystals were obtained after several weeks by
evaporation of the heated solution at room temperature.
All H atoms were located in difference electron-density maps. All H atoms
attached to C were treated as riding, with C—H = 0.95 Å (aromatic) and
with Uiso(H0 = 1.2Ueq(C). The coordination parameters of H
atoms attached to N or O were freely refined, with Uiso(H) =
1.2Ueq(N,O).
For cytosinium hydrogen sulfate, (I), the measured crystal was an inversion
twin with an approximate twin ratio of 0.6:0.4 [Flack parameter (Flack,
1983)
0.59 (8)].
For both compounds, data collection: CrysAlis CCD (Oxford Diffraction, 2008); cell refinement: CrysAlis RED (Oxford Diffraction, 2008); data reduction: CrysAlis RED (Oxford Diffraction, 2008); 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). Software used to prepare material for publication: PLATON (Spek, 2009) and Mercury (Version 1.4; Macrae et al., 2006) for (I); WinGX (Farrugia, 1999) for (II).
(I) Cytosinium hydrogen sulfate
top
Crystal data top
C4H6N3O+·HSO4− | F(000) = 432 |
Mr = 209.19 | Dx = 1.811 Mg m−3 |
Monoclinic, Cc | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: C -2yc | Cell parameters from 5769 reflections |
a = 14.676 (2) Å | θ = 3.1–32.6° |
b = 7.435 (2) Å | µ = 0.42 mm−1 |
c = 7.574 (2) Å | T = 120 K |
β = 111.79 (2)° | Prism, colourless |
V = 767.4 (3) Å3 | 0.4 × 0.3 × 0.2 mm |
Z = 4 | |
Data collection top
Nonius KappaCCD area-detector diffractometer | 2024 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.055 |
Graphite monochromator | θmax = 32.6°, θmin = 3.1° |
ϕ scans | h = −22→20 |
5769 measured reflections | k = −11→11 |
2422 independent reflections | l = −11→11 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.038 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.091 | w = 1/[σ2(Fo2) + (0.0545P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.91 | (Δ/σ)max = 0.001 |
2422 reflections | Δρmax = 0.36 e Å−3 |
134 parameters | Δρmin = −0.39 e Å−3 |
7 restraints | Absolute structure: Flack (1983), with 1410 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.59 (8) |
Crystal data top
C4H6N3O+·HSO4− | V = 767.4 (3) Å3 |
Mr = 209.19 | Z = 4 |
Monoclinic, Cc | Mo Kα radiation |
a = 14.676 (2) Å | µ = 0.42 mm−1 |
b = 7.435 (2) Å | T = 120 K |
c = 7.574 (2) Å | 0.4 × 0.3 × 0.2 mm |
β = 111.79 (2)° | |
Data collection top
Nonius KappaCCD area-detector diffractometer | 2024 reflections with I > 2σ(I) |
5769 measured reflections | Rint = 0.055 |
2422 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.038 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.091 | Δρmax = 0.36 e Å−3 |
S = 0.91 | Δρmin = −0.39 e Å−3 |
2422 reflections | Absolute structure: Flack (1983), with 1410 Friedel pairs |
134 parameters | Absolute structure parameter: 0.59 (8) |
7 restraints | |
Special details top
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 F2 against ALL reflections. The weighted R-factor
wR and goodness of fit S are based on F2, conventional
R-factors R are based on F, with F set to zero for
negative F2. The threshold expression of F2 >
σ(F2) is used only for calculating R-factors(gt) 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) top | x | y | z | Uiso*/Ueq | |
O5 | 0.39028 (12) | 0.39819 (19) | 0.5522 (3) | 0.0198 (4) | |
N1 | 0.42218 (13) | 0.7004 (3) | 0.5824 (3) | 0.0183 (5) | |
N2 | 0.18003 (13) | 0.7652 (2) | 0.1049 (3) | 0.0184 (5) | |
N3 | 0.28809 (13) | 0.5872 (2) | 0.3357 (3) | 0.0158 (5) | |
C2 | 0.36954 (15) | 0.5543 (3) | 0.4955 (3) | 0.0157 (5) | |
C4 | 0.25856 (15) | 0.7533 (2) | 0.2622 (3) | 0.0152 (5) | |
C5 | 0.31468 (15) | 0.9028 (3) | 0.3596 (3) | 0.0183 (6) | |
C6 | 0.39474 (17) | 0.8712 (3) | 0.5165 (3) | 0.0203 (6) | |
S1 | 0.60712 (4) | 0.76395 (6) | 1.04693 (6) | 0.0150 (1) | |
O1 | 0.58056 (10) | 0.6033 (2) | 0.9276 (2) | 0.0202 (4) | |
O2 | 0.71200 (11) | 0.77572 (19) | 1.1586 (2) | 0.0200 (4) | |
O3 | 0.56864 (11) | 0.9271 (2) | 0.9395 (2) | 0.0206 (5) | |
O4 | 0.56061 (13) | 0.74403 (19) | 1.2000 (3) | 0.0211 (5) | |
H1 | 0.4700 (14) | 0.683 (4) | 0.688 (2) | 0.0220* | |
H1N | 0.1471 (19) | 0.672 (2) | 0.046 (4) | 0.0221* | |
H2N | 0.1635 (18) | 0.8706 (19) | 0.057 (4) | 0.0221* | |
H3 | 0.2580 (16) | 0.490 (2) | 0.279 (3) | 0.0189* | |
H5 | 0.29631 | 1.02196 | 0.31538 | 0.0220* | |
H6 | 0.43323 | 0.97005 | 0.58327 | 0.0243* | |
H4 | 0.5008 (10) | 0.711 (4) | 1.142 (4) | 0.0253* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O5 | 0.0159 (6) | 0.0205 (7) | 0.0198 (8) | 0.0027 (5) | 0.0028 (5) | 0.0051 (6) |
N1 | 0.0152 (8) | 0.0214 (8) | 0.0145 (9) | −0.0009 (6) | 0.0012 (7) | 0.0001 (7) |
N2 | 0.0175 (9) | 0.0176 (8) | 0.0152 (9) | 0.0017 (6) | 0.0003 (7) | −0.0010 (7) |
N3 | 0.0151 (8) | 0.0141 (7) | 0.0154 (9) | −0.0005 (6) | 0.0026 (6) | −0.0010 (6) |
C2 | 0.0145 (9) | 0.0195 (9) | 0.0132 (10) | 0.0017 (7) | 0.0052 (8) | 0.0036 (7) |
C4 | 0.0148 (9) | 0.0160 (9) | 0.0144 (10) | 0.0023 (7) | 0.0051 (7) | 0.0015 (7) |
C5 | 0.0212 (11) | 0.0153 (8) | 0.0172 (11) | −0.0017 (7) | 0.0057 (9) | 0.0002 (7) |
C6 | 0.0225 (10) | 0.0177 (9) | 0.0208 (12) | −0.0045 (8) | 0.0083 (8) | −0.0017 (8) |
S1 | 0.0153 (2) | 0.0129 (2) | 0.0134 (2) | 0.0000 (2) | 0.0015 (2) | −0.0002 (2) |
O1 | 0.0225 (8) | 0.0160 (7) | 0.0162 (8) | 0.0014 (6) | 0.0003 (6) | −0.0056 (6) |
O2 | 0.0126 (6) | 0.0184 (7) | 0.0233 (9) | −0.0003 (5) | 0.0000 (6) | −0.0034 (6) |
O3 | 0.0228 (8) | 0.0141 (7) | 0.0197 (9) | 0.0011 (5) | 0.0017 (6) | 0.0052 (6) |
O4 | 0.0225 (8) | 0.0260 (8) | 0.0137 (8) | −0.0094 (6) | 0.0054 (6) | −0.0042 (6) |
Geometric parameters (Å, º) top
S1—O2 | 1.458 (2) | N3—C2 | 1.371 (3) |
S1—O3 | 1.4530 (18) | N1—H1 | 0.856 (17) |
S1—O4 | 1.556 (2) | N2—H1N | 0.87 (2) |
S1—O1 | 1.4608 (18) | N2—H2N | 0.860 (17) |
O5—C2 | 1.236 (3) | N3—H3 | 0.872 (17) |
O4—H4 | 0.86 (2) | C4—C5 | 1.417 (3) |
N1—C2 | 1.354 (3) | C5—C6 | 1.346 (3) |
N1—C6 | 1.369 (3) | C5—H5 | 0.9500 |
N2—C4 | 1.318 (3) | C6—H6 | 0.9500 |
N3—C4 | 1.358 (2) | | |
| | | |
O1—S1—O3 | 112.16 (8) | C4—N3—H3 | 121.7 (13) |
O1—S1—O4 | 107.05 (9) | C2—N3—H3 | 113.8 (14) |
O2—S1—O3 | 112.45 (9) | O5—C2—N3 | 119.7 (2) |
O2—S1—O4 | 103.55 (10) | O5—C2—N1 | 124.2 (2) |
O3—S1—O4 | 108.06 (9) | N1—C2—N3 | 116.06 (19) |
O1—S1—O2 | 112.94 (9) | N2—C4—N3 | 118.08 (17) |
S1—O4—H4 | 107.1 (18) | N2—C4—C5 | 124.23 (16) |
C2—N1—C6 | 122.0 (2) | N3—C4—C5 | 117.7 (2) |
C2—N3—C4 | 124.42 (18) | C4—C5—C6 | 118.1 (2) |
C6—N1—H1 | 121 (2) | N1—C6—C5 | 121.7 (2) |
C2—N1—H1 | 117 (2) | C4—C5—H5 | 121.00 |
C4—N2—H2N | 117.3 (18) | C6—C5—H5 | 121.00 |
H1N—N2—H2N | 120 (2) | N1—C6—H6 | 119.00 |
C4—N2—H1N | 123.0 (17) | C5—C6—H6 | 119.00 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1 | 0.856 (17) | 2.023 (18) | 2.872 (3) | 172 (3) |
N2—H1N···O3i | 0.87 (2) | 2.15 (2) | 3.007 (3) | 172 (3) |
N2—H1N···O4ii | 0.87 (2) | 2.53 (3) | 2.914 (4) | 107.8 (17) |
N2—H2N···O1iii | 0.860 (17) | 2.13 (2) | 2.966 (3) | 163 (3) |
N3—H3···O2i | 0.872 (17) | 1.835 (17) | 2.701 (3) | 172 (2) |
O4—H4···O5iv | 0.86 (2) | 1.71 (2) | 2.558 (3) | 168 (3) |
C5—H5···O2iii | 0.9500 | 2.3300 | 3.252 (3) | 165.00 |
Symmetry codes: (i) x−1/2, y−1/2, z−1; (ii) x−1/2, −y+3/2, z−3/2; (iii) x−1/2, y+1/2, z−1; (iv) x, −y+1, z+1/2. |
(II) cytosinium perchlorate
top
Crystal data top
C4H6N3O+·ClO4− | F(000) = 432 |
Mr = 211.57 | Dx = 1.859 Mg m−3 |
Orthorhombic, Pca21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2ac | Cell parameters from 11946 reflections |
a = 17.194 (2) Å | θ = 3.3–30.0° |
b = 4.940 (1) Å | µ = 0.50 mm−1 |
c = 8.901 (1) Å | T = 100 K |
V = 756.1 (2) Å3 | Prism, colourless |
Z = 4 | 0.3 × 0.2 × 0.09 mm |
Data collection top
Nonius KappaCCD area-detector diffractometer | 2146 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.022 |
Graphite monochromator | θmax = 30.0°, θmin = 3.3° |
ϕ scans | h = −24→24 |
11932 measured reflections | k = −6→6 |
2198 independent reflections | l = −12→12 |
Refinement top
Refinement on F2 | H atoms treated by a mixture of independent and constrained refinement |
Least-squares matrix: full | w = 1/[σ2(Fo2) + (0.0409P)2 + 0.0318P] where P = (Fo2 + 2Fc2)/3 |
R[F2 > 2σ(F2)] = 0.019 | (Δ/σ)max < 0.001 |
wR(F2) = 0.055 | Δρmax = 0.37 e Å−3 |
S = 1.06 | Δρmin = −0.26 e Å−3 |
2198 reflections | Absolute structure: Flack (1983), with 1166 Friedel pairs |
130 parameters | Absolute structure parameter: 0.02 (4) |
5 restraints | |
Crystal data top
C4H6N3O+·ClO4− | V = 756.1 (2) Å3 |
Mr = 211.57 | Z = 4 |
Orthorhombic, Pca21 | Mo Kα radiation |
a = 17.194 (2) Å | µ = 0.50 mm−1 |
b = 4.940 (1) Å | T = 100 K |
c = 8.901 (1) Å | 0.3 × 0.2 × 0.09 mm |
Data collection top
Nonius KappaCCD area-detector diffractometer | 2146 reflections with I > 2σ(I) |
11932 measured reflections | Rint = 0.022 |
2198 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.019 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.055 | Δρmax = 0.37 e Å−3 |
S = 1.06 | Δρmin = −0.26 e Å−3 |
2198 reflections | Absolute structure: Flack (1983), with 1166 Friedel pairs |
130 parameters | Absolute structure parameter: 0.02 (4) |
5 restraints | |
Special details top
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 F2 against ALL reflections. The weighted
R-factor wR and goodness of fit S are based on
F2, conventional R-factors R are based on F,
with F set to zero for negative F2. The threshold expression
of F2 > σ(F2) is used only for calculating
R-factors(gt) 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) top | x | y | z | Uiso*/Ueq | |
O5 | 0.20221 (5) | 0.59470 (17) | 0.62293 (10) | 0.0172 (2) | |
N1 | 0.13420 (5) | 0.87104 (18) | 0.78106 (11) | 0.0119 | |
N2 | 0.34089 (5) | 1.1738 (2) | 0.92089 (11) | 0.0138 | |
N3 | 0.26887 (5) | 0.88048 (18) | 0.77454 (10) | 0.0109 (2) | |
C2 | 0.20064 (5) | 0.7694 (2) | 0.71950 (11) | 0.0113 (2) | |
C4 | 0.27269 (6) | 1.0814 (2) | 0.87921 (11) | 0.0099 (2) | |
C5 | 0.20115 (6) | 1.1813 (2) | 0.93762 (11) | 0.0115 | |
C6 | 0.13416 (6) | 1.0703 (2) | 0.88688 (12) | 0.0121 (3) | |
Cl1 | 0.46444 (1) | 0.59970 (4) | 0.69762 (3) | 0.0103 (1) | |
O1 | 0.45167 (5) | 0.71768 (18) | 0.84416 (10) | 0.0169 (2) | |
O2 | 0.52942 (5) | 0.72577 (19) | 0.62574 (11) | 0.0193 (2) | |
O3 | 0.47855 (4) | 0.31141 (16) | 0.71251 (12) | 0.0172 (2) | |
O4 | 0.39450 (5) | 0.63886 (17) | 0.60855 (10) | 0.0165 (2) | |
H1 | 0.0906 (6) | 0.800 (3) | 0.7540 (16) | 0.0143* | |
H1N | 0.3823 (7) | 1.102 (3) | 0.8852 (17) | 0.0166* | |
H2N | 0.3429 (9) | 1.298 (3) | 0.9891 (15) | 0.0166* | |
H3 | 0.3106 (7) | 0.808 (3) | 0.7387 (16) | 0.0131* | |
H5 | 0.20046 | 1.32220 | 1.01025 | 0.0138* | |
H6 | 0.08598 | 1.13274 | 0.92596 | 0.0145* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O5 | 0.0153 (4) | 0.0181 (4) | 0.0181 (4) | −0.0008 (3) | −0.0010 (3) | −0.0091 (3) |
N1 | 0.0087 | 0.0139 | 0.0132 | −0.0006 | −0.0008 | −0.0015 |
N2 | 0.0095 | 0.0166 | 0.0152 | 0.0004 | −0.0001 | −0.0064 |
N3 | 0.0092 (4) | 0.0127 (4) | 0.0109 (4) | 0.0011 (3) | 0.0001 (3) | −0.0042 (3) |
C2 | 0.0100 (4) | 0.0126 (4) | 0.0113 (4) | −0.0003 (3) | −0.0012 (3) | −0.0010 (4) |
C4 | 0.0112 (4) | 0.0103 (4) | 0.0082 (4) | 0.0001 (3) | 0.0005 (3) | 0.0000 (3) |
C5 | 0.0126 | 0.0118 | 0.0101 | 0.0022 | 0.0005 | −0.0016 |
C6 | 0.0115 (4) | 0.0139 (5) | 0.0108 (5) | 0.0022 (4) | 0.0015 (4) | 0.0001 (3) |
Cl1 | 0.0084 (1) | 0.0106 (1) | 0.0118 (1) | 0.0004 (1) | 0.0005 (1) | −0.0008 (1) |
O1 | 0.0190 (3) | 0.0197 (4) | 0.0119 (3) | 0.0022 (3) | 0.0008 (3) | −0.0044 (3) |
O2 | 0.0148 (3) | 0.0191 (4) | 0.0239 (4) | −0.0053 (3) | 0.0081 (3) | −0.0032 (3) |
O3 | 0.0149 (3) | 0.0106 (3) | 0.0260 (4) | 0.0034 (3) | 0.0013 (4) | 0.0007 (3) |
O4 | 0.0137 (3) | 0.0194 (4) | 0.0164 (4) | 0.0033 (3) | −0.0057 (3) | −0.0006 (3) |
Geometric parameters (Å, º) top
Cl1—O2 | 1.4302 (9) | N3—C2 | 1.3847 (12) |
Cl1—O3 | 1.4509 (8) | N1—H1 | 0.862 (11) |
Cl1—O4 | 1.4533 (9) | N2—H2N | 0.864 (14) |
Cl1—O1 | 1.4454 (9) | N2—H1N | 0.857 (13) |
O5—C2 | 1.2184 (13) | N3—H3 | 0.863 (13) |
N1—C6 | 1.3624 (14) | C4—C5 | 1.4237 (14) |
N1—C2 | 1.3629 (13) | C5—C6 | 1.3533 (14) |
N2—C4 | 1.3119 (14) | C5—H5 | 0.9500 |
N3—C4 | 1.3629 (13) | C6—H6 | 0.9500 |
| | | |
O1—Cl1—O3 | 109.81 (6) | C2—N3—H3 | 114.2 (9) |
O1—Cl1—O4 | 108.23 (5) | O5—C2—N3 | 120.77 (9) |
O2—Cl1—O3 | 109.74 (5) | O5—C2—N1 | 124.28 (9) |
O2—Cl1—O4 | 110.15 (5) | N1—C2—N3 | 114.95 (9) |
O3—Cl1—O4 | 108.60 (5) | N2—C4—N3 | 119.33 (9) |
O1—Cl1—O2 | 110.29 (5) | N2—C4—C5 | 123.26 (9) |
C2—N1—C6 | 123.00 (9) | N3—C4—C5 | 117.42 (9) |
C2—N3—C4 | 124.84 (9) | C4—C5—C6 | 118.23 (9) |
C6—N1—H1 | 119.1 (9) | N1—C6—C5 | 121.54 (9) |
C2—N1—H1 | 117.8 (9) | C4—C5—H5 | 121.00 |
C4—N2—H1N | 119.6 (9) | C6—C5—H5 | 121.00 |
C4—N2—H2N | 118.8 (10) | C5—C6—H6 | 119.00 |
H1N—N2—H2N | 121.4 (14) | N1—C6—H6 | 119.00 |
C4—N3—H3 | 121.0 (9) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O3i | 0.862 (11) | 2.037 (11) | 2.8892 (11) | 169.4 (13) |
N2—H1N···O1 | 0.857 (13) | 2.272 (14) | 3.0286 (13) | 147.4 (13) |
N2—H1N···O3ii | 0.857 (13) | 2.484 (14) | 3.0830 (12) | 127.6 (12) |
N2—H2N···O2iii | 0.864 (14) | 2.513 (15) | 2.9229 (13) | 110.0 (12) |
N2—H2N···O5iv | 0.864 (14) | 2.042 (14) | 2.8473 (13) | 154.8 (14) |
N3—H3···O4 | 0.863 (13) | 2.030 (13) | 2.8764 (12) | 166.5 (13) |
C5—H5···O4iv | 0.9500 | 2.4200 | 3.1827 (13) | 137.00 |
C5—H5···O5iv | 0.9500 | 2.3700 | 3.1069 (13) | 134.00 |
C6—H6···O1v | 0.9500 | 2.5300 | 3.3298 (13) | 142.00 |
Symmetry codes: (i) x−1/2, −y+1, z; (ii) x, y+1, z; (iii) −x+1, −y+2, z+1/2; (iv) −x+1/2, y+1, z+1/2; (v) x−1/2, −y+2, z. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C4H6N3O+·HSO4− | C4H6N3O+·ClO4− |
Mr | 209.19 | 211.57 |
Crystal system, space group | Monoclinic, Cc | Orthorhombic, Pca21 |
Temperature (K) | 120 | 100 |
a, b, c (Å) | 14.676 (2), 7.435 (2), 7.574 (2) | 17.194 (2), 4.940 (1), 8.901 (1) |
α, β, γ (°) | 90, 111.79 (2), 90 | 90, 90, 90 |
V (Å3) | 767.4 (3) | 756.1 (2) |
Z | 4 | 4 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.42 | 0.50 |
Crystal size (mm) | 0.4 × 0.3 × 0.2 | 0.3 × 0.2 × 0.09 |
|
Data collection |
Diffractometer | Nonius KappaCCD area-detector diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | – | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5769, 2422, 2024 | 11932, 2198, 2146 |
Rint | 0.055 | 0.022 |
(sin θ/λ)max (Å−1) | 0.758 | 0.703 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.091, 0.91 | 0.019, 0.055, 1.06 |
No. of reflections | 2422 | 2198 |
No. of parameters | 134 | 130 |
No. of restraints | 7 | 5 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.36, −0.39 | 0.37, −0.26 |
Absolute structure | Flack (1983), with 1410 Friedel pairs | Flack (1983), with 1166 Friedel pairs |
Absolute structure parameter | 0.59 (8) | 0.02 (4) |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1 | 0.856 (17) | 2.023 (18) | 2.872 (3) | 172 (3) |
N2—H1N···O3i | 0.87 (2) | 2.15 (2) | 3.007 (3) | 172 (3) |
N2—H1N···O4ii | 0.87 (2) | 2.53 (3) | 2.914 (4) | 107.8 (17) |
N2—H2N···O1iii | 0.860 (17) | 2.13 (2) | 2.966 (3) | 163 (3) |
N3—H3···O2i | 0.872 (17) | 1.835 (17) | 2.701 (3) | 172 (2) |
O4—H4···O5iv | 0.86 (2) | 1.71 (2) | 2.558 (3) | 168 (3) |
C5—H5···O2iii | 0.9500 | 2.3300 | 3.252 (3) | 165.00 |
Symmetry codes: (i) x−1/2, y−1/2, z−1; (ii) x−1/2, −y+3/2, z−3/2; (iii) x−1/2, y+1/2, z−1; (iv) x, −y+1, z+1/2. |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O3i | 0.862 (11) | 2.037 (11) | 2.8892 (11) | 169.4 (13) |
N2—H1N···O1 | 0.857 (13) | 2.272 (14) | 3.0286 (13) | 147.4 (13) |
N2—H1N···O3ii | 0.857 (13) | 2.484 (14) | 3.0830 (12) | 127.6 (12) |
N2—H2N···O2iii | 0.864 (14) | 2.513 (15) | 2.9229 (13) | 110.0 (12) |
N2—H2N···O5iv | 0.864 (14) | 2.042 (14) | 2.8473 (13) | 154.8 (14) |
N3—H3···O4 | 0.863 (13) | 2.030 (13) | 2.8764 (12) | 166.5 (13) |
C5—H5···O4iv | 0.9500 | 2.4200 | 3.1827 (13) | 137.00 |
C5—H5···O5iv | 0.9500 | 2.3700 | 3.1069 (13) | 134.00 |
C6—H6···O1v | 0.9500 | 2.5300 | 3.3298 (13) | 142.00 |
Symmetry codes: (i) x−1/2, −y+1, z; (ii) x, y+1, z; (iii) −x+1, −y+2, z+1/2; (iv) −x+1/2, y+1, z+1/2; (v) x−1/2, −y+2, z. |
Comparison of bond lengths and angles in the cytosinium cation of (I) and (II) topBond lengths(Å) | (I) | (II) | Angle (°) | (I) | (II) |
O5—C2 | 1.236 (3) | 1.2184 (13) | C2—N1—C6 | 122.0 (2) | 123.00 (9) |
C4—N2 | 1.318 (3) | 1.3119 (14) | C2—N3—C4 | 124.42 (18) | 124.84 (9) |
C4—N3 | 1.358 (2) | 1.3629 (13) | O5- C2—N3 | 119.7 (2) | 120.77 (9) |
C4—C5 | 1.417 (3) | 1.4237 (14) | O5—C2—N1 | 124.2 (2) | 124.28 (9) |
N3—C2 | 1.371 (3) | 1.3847 (12) | N1—C2—N3 | 116.06 (19) | 114.95 (9) |
C5—C6 | 1.346 (3) | 1.3533 (14) | N2—C4—N3 | 118.08 (17) | 119.33 (9) |
N1—C6 | 1.369 (3) | 1.3624 (14) | N2—C4—C5 | 124.23 (16) | 123.26 (9) |
N1—C2 | 1.354 (3) | 1.3629 (13) | N3—C4—C5 | 117.7 (2) | 117.42 (9) |
| | | C4—C5—C6 | 118.1 (2) | 118.23 (9) |
| | | N1—C6—C5 | 121.7 (2) | 121.54 (9) |
The present work is part of a general structural study of purine and pyrimidine base salt compounds and their hydrogen-bonding patterns. A series of similar compounds has been reported previously: cytosinium nitrate (Cherouana, Bouchouit et al., 2003), adeninium perchlorate (Bendjeddou et al., 2003), guaninium sulfate (Cherouana, Benali-Cherif et al., 2003) and cytosinium oxalate monohydrate (Bouchouit et al., 2005).
Hydrogen bonding dominates the formation of secondary structure in proteins, and its importance in the structure and function of biomolecules has been stressed by Jeffrey & Saenger (1991).
The nucleic acid base used in this study, 6-aminopyrimidine-2-one (cytosine), is one of the pyrimidine bases found in deoxyribonucleic acids and it has been the subject of investigations aimed at studying the electrostatic properties of its monohydrate form (Weber & Craven, 1990). In our search for new salt compounds and investigation of the functionality of biological systems, we have prepared the three compounds cytosinium hydrogen sulfate, (I), cytosinium perchlorate, (II), and cytosinium nitrate in order to study the important role that hydrogen bonding plays in these structures.
The crystal structure of cytosinium nitrate was reported by Cherouana, Bouchouit et al. (2003). It consists of parallel mixed cation–anion sheets stacked along [101]. These sheets feature moderate N—H···O and weak C—H···O hydrogen bonds with dominant Rda(n) graph sets (Bernstein et al., 1995). Interaction between sheets is facilitated by van der Waals interactions.
In both structures (I) and (II), the organic part is in its cationic form. As observed in all structures containing this cation (Kindberg & Amma, 1975), the cytosine is mono-protonated at N3 and this is clearly evidenced by the bond-length and -angle variations involving atom N3 (Table 1). Bond lengths in the tetrahedral hydrogen sulfate group also indicate the position of the H atom. There are three short S—O bonds of 1.4608 (18), 1.458 (2) and 1.4530 (18) Å to terminal atoms O1, O2 and O3, respectively, and one longer bond of 1.556 (2) Å to atom O4, which is bound to atom H4. In the perchlorate, the Cl atom is linked via four short bonds of 1.4454 (9), 1.4302 (9), 1.4509 (9) and 1.4533 (9) Å to terminal atoms O3, O4 O5 and O6, respectively, and this is consistent with the absence of a proton in this anion. The asymmetric unit of (I) consists of a protonated cytosine ring and a hydrogen sulfate anion, while that of (II) consists of a protonated cytosine ring and a perchlorate anion (Figs. 1 and 2).
Supramolecular aggregations in (I) and (II) are based on three-dimensional hydrogen-bonding networks that are dominated by N—H···O hydrogen bonds. Hence, only one O—H···O and one C—H···O [in (I)], and three C—H···O [in (II)] unique hydrogen bonds are observed (Tables 2 and 3). It is noteworthy that hydrogen bonds between cytosinium rings (Fig. 3) are absent in (I), contrary to what was observed in cytosine (Barker & Marsh, 1964), cytosine monohydrate (Jeffrey & Kinoshita, 1963), cytosine hydrochloride (Mandel, 1977), and in the structure of (II) reported here. This is due to the presence of the hydrogen sulfate H atom, which separates the two cations by virtue of the anion-to-cation O—H···O hydrogen bond. The protonated cytosine rings are planar, with the greatest deviation from the least-squares plane being 0.0429 (21) Å for the amino N atom in (I) and 0.077 (10) Å in (II). The amino H atoms also lie in this plane. The pyrimidine ring bond distances are, in general, not significantly different from those found in cytosine or cytosine monohydrate. In both structures, the cytosinium cation acts as a hydrogen-bond donor via its N and C atoms (N1, N2, N3, C4 and C5). The hydrogen sulfate anion H atom acts as an O—H···O hydrogen-bond acceptor (Tables 2 and 3).
In (I), the combination of H atoms of the amino group with two other different hydrogen bonds (N3—H3···O2 and C5—H5···O2) generates the same type of binary graph-set, R22(8) c→, d← and R22(8) e→, f← (Grell et al., 1999). The hydrogen-bonding binary graph-set is essentially formed by infinite chains with a maximum degree of ten. The two types of rings observed in this graph are those cited below. The propagation of these infinite chains, and their combination with rings formed by N2—H2N···O1 and C5—H5···O2 hydrogen bonds, generates chains of edge-fused R44(18) b→c←e→b←d→ f← rings running along [102] (Fig. 4a). These chains of rings are interlinked along [110] by mixed chains formed by the two binary rings R22(8) c→, d← and R22(8) e→, f← using H atoms of the amino group (see below). The combination of these three types of rings leads to layers which are stacked along [101]. The junction between these layers is ensured by the only O—H···O hydrogen bond present in the structure, for which the hydrogen sulfate anion is the donor and the cytosinium cation the acceptor (Fig. 4b). The structure of cytosinium hydrogen sulfate can thus be described as a succession of mixed layers parallel to their stacking direction [102], linked by strong O—H···O hydrogen bonds.
The structural intgegrity of (II) is maintained by a three-dimensional hydrogen-bonding network between cations, and between cations and anions. A very strong N3—H3···O4 hydrogen bond is observed. The cytosine cation is linked to a single perchlorate ion by N—H···O and C—H···O hydrogen bonds. All hydrogen bonds present in this structure are three-centred except N1—H1···O4 and C6—H6···O1. Cation–cation N—H···O and C—H···O hydrogen bonds present in this structure form two symmetrically crossed infinite chains of rings with an R12(6) d→h← graph-set motif. These chains are crystallographically linked by the a glide plane, and the angle between them is about 87.1° (Fig. 6). The junction between the cationic chains occurs via the perchlorate anion as a result of cation–anion hydrogen bonds. The crystal structure is thus based on crossed mixed cation–anion layers in a three-dimensional hydrogen-bonded network. These layers are formed by rings of hydrogen bonds involving the terminal –NH2 group, atoms N3 and C5 as donors, and O atoms as acceptors, to form chains of edge-fused rings R22(6) f→ g← h→ and R21(6) d→ h← stacked along [021]. These chains are interlinked by R23(8) a→e←d→ and R22(8) e→f→ rings (Fig. 6a). Such rings are also found along [012], crossing the first sheet of chains of rings to form an infinite three-dimensional hydrogen-bonded network; this can be understood as the result of the geometry of the perchlorate anion acceptor atoms (Fig. 6b).
In an attempt to study the influence of anion substitution (Fig. 7) on the graph-set analysis, we used the same three reactions, giving three similar products with three different [Text missing?].
The substitution of a tetrahedral hydrogen sulfate anion by a planar nitrate anion or a tetrahedral perchlorate anion does not affect the general packing features of the crystal structure. Indeed, the same mixed two-dimensional layers are observed in the two compounds. These layers are parallel to [102] in (I), and crossed by 86.91° in (II). However, the difference in geometry between the two anions, and the absence of H atoms in the perchlorate anions, directly affects the hydrogen bonds in the two structures. The construction of hydrogen-bonding binary graph-sets for the two compounds yields the same rings for the two crystal structures, with a variation in the degree n. However, in the case of (II) we observe an additional such R12(6) ring. This additional binary graph-set is generated by cytosinium–cytosinium hydrogen bonds and this is due to the absence of H atoms on the anion. The structures of the three cytosinium compounds can thus be described as two-dimensional mixed sheets formed by a succession of edge-fused Rda(n) rings. The orientation of these sheets depends on the geometry of the acceptor atoms on the anion. In the hydrogen sulfate and nitrate anions, the geometry of the acceptor atoms is identical and sheets have the same parallel orientation. However, the absence of an H atom in the nitrate anion makes its structure less compact than the others. This is due to the junction between the mixed layers, which is ensured by the strongest O—H···O hydrogen bond [2.558 (3) Å] in cytosinium hydrogen sulfate, and by van der Waals interactions between the cations [3.09 (2) Å] in cytosinium nitrate. The tetrahedral geometry of the acceptor atoms of the perchlorate anion causes these sheets to be crossed at an angle of 86.91°. The absence of an H atom in the perchlorate and nitrate anions allows merging of the cytosinium cations. The interactions observed between the two cations belonging to the same layer (C5···O5 = 3.965 Å and C6···O5 = 3.930 Å) in (I) are shortened, and moderate the N—H···O hydrogen bonds in (II) [N2···O5 = 2.8473 (13) Å].
The crystal structures of the three cytosinium salts are thus similar and can be described as a succession of cation–anion mixed sheets held together by strong hydrogen bonds. The study of anion substitution in these structures allows us to conclude that the geometry of the acceptor atoms and the presence or absence of H atoms in the anionic part directly affect the packing of sheets in the crystal structure, as well as the hydrogen-bonded graph-set pattern.