In cytosinium succinate (systematic name: 4-amino-2-oxo-2,3-dihydropyrimidin-1-ium 3-carboxypropanoate), C
4H
6N
3O
+·C
4H
5O
4−, (I), the cytosinium cation forms one-dimensional self-assembling patterns by intermolecular N—H
O hydrogen bonding, while in cytosinium 4-nitrobenzoate cytosine monohydrate [systematic name: 4-amino-2-oxo-2,3-dihydropyrimidin-1-ium 4-nitrobenzoate 4-aminopyrimidin-2(1
H)-one solvate monohydrate], C
4H
6N
3O
+·C
7H
4NO
4−·C
4H
5N
3O·H
2O, (II), the cytosinium–cytosine base pair, held together by triple hydrogen bonds, leads to one-dimensional polymeric ribbons
via double N—H
O hydrogen bonds. This study illustrates clearly the different alignment of cytosine molecules in the crystal packing and their ability to form supramolecular hydrogen-bonded networks with the anions.
Supporting information
CCDC references: 707218; 707219
To obtain crystals of (I) suitable for X-ray study, cytosine (0.111 g, 1 mmol)
and succinic acid (0.118 g, 1 mmol) were dissolved in water (10 ml) and the
solution was allowed to evaporate slowly. Crystals of (II) were obtained by
slow evaporation of an equimolar solution of cytosine (0.111 g, 2 mmol) and
4-nitrobenzoic acid (0.167 g, 1 mmol) in water (20 ml).
All N- and O-bound H atoms were located in a difference Fourier map and their
positions and isotropic parameters were refined. All other H atoms were
located in a difference density map but were positioned geometrically and
included as riding atoms, with C—H distances in the range 0.93–0.97 Å,
and with Uiso(H) = 1.2Ueq(C).
For both compounds, data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL/PC (Sheldrick, 2008) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).
(I) 4-amino-2-oxo-2,3-dihydropyrimidin-1-ium 3-carboxypropanoate
top
Crystal data top
C4H6N3O+·C4H5O4− | F(000) = 960 |
Mr = 229.20 | Dx = 1.576 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 2934 reflections |
a = 15.666 (3) Å | θ = 3.0–27.7° |
b = 6.6959 (9) Å | µ = 0.13 mm−1 |
c = 18.726 (3) Å | T = 294 K |
β = 100.480 (4)° | Block, colorless |
V = 1931.5 (5) Å3 | 0.23 × 0.17 × 0.13 mm |
Z = 8 | |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 1607 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.021 |
Graphite monochromator | θmax = 25.0°, θmin = 2.2° |
ω scan | h = −18→18 |
8824 measured reflections | k = −7→7 |
1697 independent reflections | l = −22→22 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.108 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.10 | w = 1/[σ2(Fo2) + (0.0619P)2 + 1.1366P] where P = (Fo2 + 2Fc2)/3 |
1697 reflections | (Δ/σ)max = 0.001 |
165 parameters | Δρmax = 0.22 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
Crystal data top
C4H6N3O+·C4H5O4− | V = 1931.5 (5) Å3 |
Mr = 229.20 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 15.666 (3) Å | µ = 0.13 mm−1 |
b = 6.6959 (9) Å | T = 294 K |
c = 18.726 (3) Å | 0.23 × 0.17 × 0.13 mm |
β = 100.480 (4)° | |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 1607 reflections with I > 2σ(I) |
8824 measured reflections | Rint = 0.021 |
1697 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.108 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.10 | Δρmax = 0.22 e Å−3 |
1697 reflections | Δρmin = −0.19 e Å−3 |
165 parameters | |
Special details top
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C2 | 0.24296 (11) | 0.9672 (2) | 0.36715 (9) | 0.0431 (4) | |
C4 | 0.27374 (8) | 0.6259 (2) | 0.40047 (7) | 0.0293 (3) | |
C5 | 0.21523 (9) | 0.5640 (2) | 0.33688 (8) | 0.0339 (3) | |
H5 | 0.2055 | 0.4293 | 0.3263 | 0.041* | |
C6 | 0.17464 (9) | 0.7058 (2) | 0.29278 (8) | 0.0348 (3) | |
H6 | 0.1365 | 0.6678 | 0.2510 | 0.042* | |
N1 | 0.18750 (8) | 0.9025 (2) | 0.30726 (7) | 0.0379 (3) | |
H1N | 0.1598 (14) | 0.997 (4) | 0.2797 (12) | 0.067 (6)* | |
N3 | 0.28423 (8) | 0.82252 (19) | 0.41264 (7) | 0.0342 (3) | |
H3N | 0.3223 (14) | 0.874 (4) | 0.4538 (12) | 0.067 (6)* | |
N7 | 0.31822 (9) | 0.5027 (2) | 0.44761 (7) | 0.0381 (3) | |
H7N | 0.3552 (12) | 0.551 (3) | 0.4872 (10) | 0.048 (5)* | |
H8N | 0.3103 (13) | 0.372 (4) | 0.4406 (11) | 0.062 (6)* | |
O8 | 0.25613 (11) | 1.14294 (19) | 0.37986 (8) | 0.0851 (6) | |
C11 | 0.43913 (9) | 0.8917 (2) | 0.56554 (7) | 0.0323 (3) | |
C12 | 0.49945 (9) | 1.0063 (2) | 0.62368 (8) | 0.0342 (4) | |
H12A | 0.4889 | 0.9647 | 0.6709 | 0.041* | |
H12B | 0.5589 | 0.9719 | 0.6210 | 0.041* | |
C13 | 0.48910 (9) | 1.2286 (2) | 0.61737 (8) | 0.0354 (4) | |
H13B | 0.5001 | 1.2696 | 0.5702 | 0.042* | |
H13A | 0.4293 | 1.2621 | 0.6193 | 0.042* | |
C14 | 0.54742 (9) | 1.3459 (2) | 0.67471 (7) | 0.0330 (3) | |
O9 | 0.39163 (7) | 0.98932 (16) | 0.51724 (6) | 0.0445 (3) | |
O10 | 0.43902 (7) | 0.70284 (16) | 0.56806 (6) | 0.0432 (3) | |
O15 | 0.59984 (7) | 1.26888 (18) | 0.72319 (6) | 0.0441 (3) | |
O16 | 0.54141 (8) | 1.54080 (17) | 0.67157 (6) | 0.0446 (3) | |
H16O | 0.4996 (15) | 1.600 (4) | 0.6292 (13) | 0.078 (7)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C2 | 0.0540 (9) | 0.0247 (8) | 0.0411 (9) | −0.0002 (6) | −0.0161 (7) | 0.0012 (6) |
C4 | 0.0318 (7) | 0.0244 (7) | 0.0293 (7) | −0.0007 (5) | −0.0010 (5) | −0.0002 (5) |
C5 | 0.0392 (8) | 0.0253 (7) | 0.0326 (7) | −0.0030 (6) | −0.0056 (6) | −0.0028 (6) |
C6 | 0.0370 (7) | 0.0329 (8) | 0.0298 (7) | −0.0038 (6) | −0.0064 (6) | −0.0023 (6) |
N1 | 0.0445 (7) | 0.0282 (7) | 0.0337 (7) | 0.0002 (5) | −0.0123 (5) | 0.0040 (5) |
N3 | 0.0407 (7) | 0.0239 (6) | 0.0315 (6) | −0.0012 (5) | −0.0106 (5) | −0.0015 (5) |
N7 | 0.0461 (7) | 0.0243 (7) | 0.0367 (7) | 0.0008 (5) | −0.0116 (6) | 0.0006 (5) |
O8 | 0.1243 (13) | 0.0215 (7) | 0.0801 (10) | −0.0012 (7) | −0.0598 (9) | −0.0007 (6) |
C11 | 0.0338 (7) | 0.0312 (8) | 0.0285 (7) | −0.0030 (6) | −0.0033 (6) | −0.0022 (6) |
C12 | 0.0344 (7) | 0.0336 (8) | 0.0302 (7) | −0.0038 (6) | −0.0056 (6) | −0.0022 (6) |
C13 | 0.0373 (7) | 0.0319 (8) | 0.0316 (7) | −0.0023 (6) | −0.0082 (6) | −0.0030 (6) |
C14 | 0.0347 (7) | 0.0331 (8) | 0.0278 (7) | −0.0026 (6) | −0.0035 (5) | −0.0031 (6) |
O9 | 0.0518 (7) | 0.0330 (6) | 0.0386 (6) | −0.0030 (5) | −0.0190 (5) | −0.0015 (5) |
O10 | 0.0531 (7) | 0.0283 (6) | 0.0406 (6) | −0.0033 (5) | −0.0118 (5) | −0.0026 (4) |
O15 | 0.0472 (6) | 0.0365 (7) | 0.0389 (6) | −0.0005 (5) | −0.0174 (5) | −0.0024 (5) |
O16 | 0.0551 (7) | 0.0301 (6) | 0.0402 (6) | −0.0029 (5) | −0.0140 (5) | −0.0036 (5) |
Geometric parameters (Å, º) top
C2—O8 | 1.211 (2) | N7—H8N | 0.89 (3) |
C2—N1 | 1.3586 (19) | C11—O9 | 1.2468 (18) |
C2—N3 | 1.372 (2) | C11—O10 | 1.2653 (19) |
C4—N7 | 1.3125 (19) | C11—C12 | 1.5141 (19) |
C4—N3 | 1.3408 (19) | C12—C13 | 1.500 (2) |
C4—C5 | 1.4258 (19) | C12—H12A | 0.9700 |
C5—C6 | 1.341 (2) | C12—H12B | 0.9700 |
C5—H5 | 0.9300 | C13—C14 | 1.4993 (19) |
C6—N1 | 1.352 (2) | C13—H13B | 0.9700 |
C6—H6 | 0.9300 | C13—H13A | 0.9700 |
N1—H1N | 0.88 (2) | C14—O15 | 1.2220 (18) |
N3—H3N | 0.95 (2) | C14—O16 | 1.3089 (19) |
N7—H7N | 0.91 (2) | O16—H16O | 1.01 (3) |
| | | |
O8—C2—N1 | 122.20 (15) | H7N—N7—H8N | 121.4 (18) |
O8—C2—N3 | 121.34 (14) | O9—C11—O10 | 123.12 (13) |
N1—C2—N3 | 116.46 (14) | O9—C11—C12 | 117.89 (13) |
N7—C4—N3 | 118.00 (13) | O10—C11—C12 | 118.98 (12) |
N7—C4—C5 | 124.10 (13) | C13—C12—C11 | 113.71 (12) |
N3—C4—C5 | 117.90 (13) | C13—C12—H12A | 108.8 |
C6—C5—C4 | 117.97 (13) | C11—C12—H12A | 108.8 |
C6—C5—H5 | 121.0 | C13—C12—H12B | 108.8 |
C4—C5—H5 | 121.0 | C11—C12—H12B | 108.8 |
C5—C6—N1 | 121.99 (14) | H12A—C12—H12B | 107.7 |
C5—C6—H6 | 119.0 | C14—C13—C12 | 114.88 (13) |
N1—C6—H6 | 119.0 | C14—C13—H13B | 108.5 |
C6—N1—C2 | 121.72 (13) | C12—C13—H13B | 108.5 |
C6—N1—H1N | 122.9 (15) | C14—C13—H13A | 108.5 |
C2—N1—H1N | 115.3 (15) | C12—C13—H13A | 108.5 |
C4—N3—C2 | 123.95 (13) | H13B—C13—H13A | 107.5 |
C4—N3—H3N | 122.4 (14) | O15—C14—O16 | 119.16 (13) |
C2—N3—H3N | 113.6 (15) | O15—C14—C13 | 123.40 (14) |
C4—N7—H7N | 120.2 (12) | O16—C14—C13 | 117.43 (12) |
C4—N7—H8N | 118.4 (14) | C14—O16—H16O | 117.3 (14) |
| | | |
N7—C4—C5—C6 | −179.22 (14) | O8—C2—N3—C4 | −178.39 (18) |
N3—C4—C5—C6 | 0.5 (2) | N1—C2—N3—C4 | 1.1 (2) |
C4—C5—C6—N1 | −0.3 (2) | O9—C11—C12—C13 | 3.78 (19) |
C5—C6—N1—C2 | 0.6 (2) | O10—C11—C12—C13 | −176.15 (13) |
O8—C2—N1—C6 | 178.57 (19) | C11—C12—C13—C14 | 179.41 (11) |
N3—C2—N1—C6 | −0.9 (2) | C12—C13—C14—O15 | 0.1 (2) |
N7—C4—N3—C2 | 178.81 (14) | C12—C13—C14—O16 | 179.66 (13) |
C5—C4—N3—C2 | −0.9 (2) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O15i | 0.88 (2) | 2.02 (2) | 2.9018 (18) | 175 (2) |
N3—H3N···O9 | 0.95 (2) | 1.65 (2) | 2.5916 (15) | 172 (2) |
N7—H7N···O10 | 0.91 (2) | 2.08 (2) | 2.9854 (18) | 171.0 (17) |
N7—H8N···O8ii | 0.89 (3) | 2.00 (2) | 2.8122 (19) | 150.5 (19) |
O16—H16O···O10iii | 1.01 (3) | 1.51 (3) | 2.5250 (16) | 176 (2) |
C5—H5···O8ii | 0.93 | 2.24 | 2.970 (2) | 135 |
Symmetry codes: (i) x−1/2, −y+5/2, z−1/2; (ii) x, y−1, z; (iii) x, y+1, z. |
(II) 4-amino-2-oxo-2,3-dihydropyrimidin-1-ium
4-nitrobenzoate 4-aminopyrimidin-2(1H)-one solvate monohydrate
top
Crystal data top
C4H6N3O+·C7H4NO4−·C4H5N3O·H2O | Z = 2 |
Mr = 407.36 | F(000) = 424 |
Triclinic, P1 | Dx = 1.539 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.7154 (14) Å | Cell parameters from 7202 reflections |
b = 7.4036 (16) Å | θ = 2.2–28.0° |
c = 19.228 (4) Å | µ = 0.13 mm−1 |
α = 85.525 (4)° | T = 294 K |
β = 87.576 (4)° | Block, colorless |
γ = 67.279 (3)° | 0.19 × 0.16 × 0.08 mm |
V = 879.0 (3) Å3 | |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 2570 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.044 |
Graphite monochromator | θmax = 25.0°, θmin = 1.1° |
ω scan | h = −7→7 |
8258 measured reflections | k = −8→8 |
3064 independent reflections | l = −22→22 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.070 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.209 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.10 | w = 1/[σ2(Fo2) + (0.1347P)2 + 0.1481P] where P = (Fo2 + 2Fc2)/3 |
3064 reflections | (Δ/σ)max < 0.001 |
298 parameters | Δρmax = 0.43 e Å−3 |
0 restraints | Δρmin = −0.45 e Å−3 |
Crystal data top
C4H6N3O+·C7H4NO4−·C4H5N3O·H2O | γ = 67.279 (3)° |
Mr = 407.36 | V = 879.0 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 6.7154 (14) Å | Mo Kα radiation |
b = 7.4036 (16) Å | µ = 0.13 mm−1 |
c = 19.228 (4) Å | T = 294 K |
α = 85.525 (4)° | 0.19 × 0.16 × 0.08 mm |
β = 87.576 (4)° | |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 2570 reflections with I > 2σ(I) |
8258 measured reflections | Rint = 0.044 |
3064 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.070 | 0 restraints |
wR(F2) = 0.209 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.10 | Δρmax = 0.43 e Å−3 |
3064 reflections | Δρmin = −0.45 e Å−3 |
298 parameters | |
Special details top
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C2A | 0.7429 (4) | 0.1448 (3) | 0.41776 (12) | 0.0295 (5) | |
C4A | 0.7629 (3) | −0.1877 (3) | 0.42401 (12) | 0.0287 (5) | |
C5A | 0.7629 (4) | −0.1816 (4) | 0.35042 (12) | 0.0340 (6) | |
H5A | 0.7711 | −0.2902 | 0.3274 | 0.041* | |
C6A | 0.7508 (4) | −0.0155 (4) | 0.31490 (13) | 0.0352 (6) | |
H6A | 0.7502 | −0.0091 | 0.2664 | 0.042* | |
N1A | 0.7395 (3) | 0.1446 (3) | 0.34758 (11) | 0.0355 (5) | |
H1A | 0.721 (6) | 0.256 (6) | 0.320 (2) | 0.069 (10)* | |
N3A | 0.7537 (3) | −0.0254 (3) | 0.45455 (10) | 0.0293 (5) | |
H3A | 0.756 (5) | −0.024 (5) | 0.5046 (19) | 0.059 (9)* | |
N7A | 0.7693 (4) | −0.3395 (3) | 0.46420 (12) | 0.0369 (6) | |
O8A | 0.7359 (3) | 0.2871 (2) | 0.44812 (9) | 0.0411 (5) | |
H7A | 0.772 (4) | −0.442 (5) | 0.4462 (15) | 0.043 (8)* | |
H8A | 0.767 (4) | −0.333 (4) | 0.5152 (15) | 0.035 (7)* | |
C2B | 0.7662 (4) | −0.2006 (3) | 0.63813 (12) | 0.0276 (5) | |
C4B | 0.7400 (3) | 0.1223 (3) | 0.63833 (12) | 0.0280 (5) | |
C5B | 0.7524 (4) | 0.1080 (4) | 0.71189 (13) | 0.0349 (6) | |
H5B | 0.7499 | 0.2125 | 0.7363 | 0.042* | |
C6B | 0.7679 (4) | −0.0635 (4) | 0.74500 (13) | 0.0365 (6) | |
H6B | 0.7746 | −0.0784 | 0.7934 | 0.044* | |
N1B | 0.7739 (3) | −0.2145 (3) | 0.70870 (10) | 0.0352 (5) | |
H1B | 0.770 (6) | −0.317 (6) | 0.730 (2) | 0.068 (10)* | |
N3B | 0.7508 (3) | −0.0296 (3) | 0.60271 (10) | 0.0280 (5) | |
N7B | 0.7188 (4) | 0.2883 (3) | 0.60162 (13) | 0.0386 (6) | |
O8B | 0.7726 (3) | −0.3444 (2) | 0.60712 (9) | 0.0400 (5) | |
H7B | 0.713 (5) | 0.386 (5) | 0.6241 (17) | 0.057 (9)* | |
H8B | 0.714 (5) | 0.294 (4) | 0.5552 (17) | 0.044 (8)* | |
C12 | 0.8120 (4) | −0.6443 (4) | 0.90808 (13) | 0.0396 (6) | |
C13 | 0.9478 (5) | −0.6793 (4) | 0.96393 (15) | 0.0496 (7) | |
H13 | 1.0716 | −0.6517 | 0.9580 | 0.060* | |
C14 | 0.9056 (6) | −0.7532 (5) | 1.02753 (15) | 0.0584 (8) | |
H14 | 0.9971 | −0.7742 | 1.0649 | 0.070* | |
C15 | 0.7226 (5) | −0.7960 (4) | 1.03467 (14) | 0.0503 (8) | |
C16 | 0.5867 (5) | −0.7661 (5) | 0.98061 (17) | 0.0556 (8) | |
H16 | 0.4649 | −0.7966 | 0.9866 | 0.067* | |
C17 | 0.6309 (5) | −0.6902 (4) | 0.91697 (15) | 0.0504 (7) | |
H17 | 0.5388 | −0.6698 | 0.8798 | 0.060* | |
C11 | 0.8610 (5) | −0.5530 (4) | 0.83995 (14) | 0.0445 (7) | |
N18 | 0.6759 (7) | −0.8751 (4) | 1.10258 (15) | 0.0748 (10) | |
O9 | 1.0263 (4) | −0.5173 (4) | 0.83713 (12) | 0.0805 (8) | |
O10 | 0.7289 (3) | −0.5132 (3) | 0.79171 (9) | 0.0497 (6) | |
O20 | 0.5082 (7) | −0.9016 (5) | 1.10923 (16) | 0.1112 (12) | |
O19 | 0.8051 (7) | −0.9097 (5) | 1.14913 (14) | 0.1159 (13) | |
O1W | 0.6864 (4) | 0.4584 (3) | 0.25694 (11) | 0.0500 (6) | |
H1W | 0.570 (5) | 0.469 (4) | 0.2305 (17) | 0.049 (8)* | |
H2W | 0.771 (7) | 0.477 (6) | 0.225 (2) | 0.091 (14)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C2A | 0.0312 (12) | 0.0247 (12) | 0.0348 (13) | −0.0140 (10) | 0.0018 (9) | 0.0004 (9) |
C4A | 0.0295 (12) | 0.0271 (12) | 0.0336 (12) | −0.0147 (9) | −0.0001 (9) | −0.0057 (9) |
C5A | 0.0390 (13) | 0.0332 (13) | 0.0345 (13) | −0.0177 (11) | 0.0005 (10) | −0.0092 (10) |
C6A | 0.0344 (13) | 0.0444 (15) | 0.0311 (12) | −0.0191 (11) | 0.0008 (10) | −0.0071 (11) |
N1A | 0.0411 (12) | 0.0346 (12) | 0.0330 (11) | −0.0181 (10) | 0.0002 (9) | 0.0033 (9) |
N3A | 0.0378 (11) | 0.0245 (11) | 0.0299 (11) | −0.0164 (8) | −0.0008 (8) | −0.0033 (8) |
N7A | 0.0575 (14) | 0.0228 (11) | 0.0379 (13) | −0.0230 (10) | −0.0007 (10) | −0.0060 (9) |
O8A | 0.0622 (12) | 0.0247 (9) | 0.0444 (10) | −0.0251 (8) | 0.0004 (8) | −0.0041 (7) |
C2B | 0.0332 (12) | 0.0217 (11) | 0.0320 (12) | −0.0149 (9) | 0.0000 (9) | −0.0022 (9) |
C4B | 0.0258 (11) | 0.0217 (11) | 0.0390 (13) | −0.0116 (9) | 0.0008 (9) | −0.0048 (9) |
C5B | 0.0406 (14) | 0.0295 (13) | 0.0387 (13) | −0.0162 (11) | −0.0005 (10) | −0.0120 (10) |
C6B | 0.0427 (14) | 0.0415 (15) | 0.0306 (12) | −0.0213 (11) | −0.0015 (10) | −0.0066 (10) |
N1B | 0.0504 (13) | 0.0320 (12) | 0.0306 (11) | −0.0246 (10) | −0.0017 (9) | 0.0024 (9) |
N3B | 0.0342 (11) | 0.0222 (10) | 0.0317 (10) | −0.0149 (8) | 0.0006 (8) | −0.0044 (8) |
N7B | 0.0567 (14) | 0.0218 (11) | 0.0434 (14) | −0.0208 (10) | −0.0040 (10) | −0.0056 (9) |
O8B | 0.0670 (12) | 0.0264 (9) | 0.0366 (10) | −0.0284 (9) | −0.0003 (8) | −0.0047 (7) |
C12 | 0.0561 (16) | 0.0327 (14) | 0.0354 (13) | −0.0228 (12) | 0.0027 (11) | −0.0050 (10) |
C13 | 0.0610 (18) | 0.0522 (17) | 0.0448 (16) | −0.0322 (15) | −0.0040 (13) | 0.0005 (13) |
C14 | 0.086 (2) | 0.060 (2) | 0.0358 (15) | −0.0351 (18) | −0.0109 (14) | 0.0032 (13) |
C15 | 0.083 (2) | 0.0368 (16) | 0.0335 (14) | −0.0270 (15) | 0.0111 (14) | −0.0034 (11) |
C16 | 0.0612 (18) | 0.0519 (18) | 0.0613 (19) | −0.0322 (15) | 0.0085 (15) | 0.0035 (14) |
C17 | 0.0615 (18) | 0.0527 (18) | 0.0457 (16) | −0.0328 (15) | −0.0068 (13) | 0.0070 (13) |
C11 | 0.0612 (17) | 0.0425 (16) | 0.0379 (14) | −0.0296 (13) | 0.0013 (13) | −0.0001 (12) |
N18 | 0.135 (3) | 0.0566 (18) | 0.0426 (17) | −0.0493 (19) | 0.0248 (18) | −0.0073 (13) |
O9 | 0.0813 (17) | 0.128 (2) | 0.0586 (14) | −0.0745 (17) | −0.0050 (12) | 0.0229 (14) |
O10 | 0.0778 (14) | 0.0474 (12) | 0.0380 (10) | −0.0404 (10) | −0.0100 (9) | 0.0068 (8) |
O20 | 0.158 (3) | 0.125 (3) | 0.0767 (19) | −0.089 (3) | 0.046 (2) | −0.0007 (17) |
O19 | 0.205 (4) | 0.124 (3) | 0.0387 (15) | −0.087 (3) | −0.0048 (19) | 0.0130 (15) |
O1W | 0.0575 (13) | 0.0507 (13) | 0.0433 (11) | −0.0250 (10) | −0.0020 (10) | 0.0107 (9) |
Geometric parameters (Å, º) top
C2A—O8A | 1.228 (3) | C6B—H6B | 0.9300 |
C2A—N1A | 1.351 (3) | N1B—H1B | 0.85 (4) |
C2A—N3A | 1.374 (3) | N7B—H7B | 0.86 (4) |
C4A—N7A | 1.301 (3) | N7B—H8B | 0.89 (3) |
C4A—N3A | 1.357 (3) | C12—C13 | 1.382 (4) |
C4A—C5A | 1.412 (3) | C12—C17 | 1.385 (4) |
C5A—C6A | 1.335 (4) | C12—C11 | 1.509 (4) |
C5A—H5A | 0.9300 | C13—C14 | 1.364 (4) |
C6A—N1A | 1.359 (3) | C13—H13 | 0.9300 |
C6A—H6A | 0.9300 | C14—C15 | 1.382 (5) |
N1A—H1A | 0.91 (4) | C14—H14 | 0.9300 |
N3A—H3A | 0.97 (4) | C15—C16 | 1.360 (4) |
N7A—H7A | 0.85 (3) | C15—N18 | 1.461 (4) |
N7A—H8A | 0.98 (3) | C16—C17 | 1.375 (4) |
C2B—O8B | 1.246 (3) | C16—H16 | 0.9300 |
C2B—N1B | 1.354 (3) | C17—H17 | 0.9300 |
C2B—N3B | 1.360 (3) | C11—O9 | 1.235 (4) |
C4B—N7B | 1.329 (3) | C11—O10 | 1.248 (3) |
C4B—N3B | 1.339 (3) | N18—O19 | 1.216 (5) |
C4B—C5B | 1.414 (3) | N18—O20 | 1.216 (5) |
C5B—C6B | 1.343 (4) | O1W—H1W | 0.92 (3) |
C5B—H5B | 0.9300 | O1W—H2W | 0.85 (5) |
C6B—N1B | 1.350 (3) | | |
| | | |
O8A—C2A—N1A | 123.2 (2) | C6B—N1B—C2B | 121.9 (2) |
O8A—C2A—N3A | 120.8 (2) | C6B—N1B—H1B | 120 (2) |
N1A—C2A—N3A | 116.0 (2) | C2B—N1B—H1B | 118 (2) |
N7A—C4A—N3A | 118.1 (2) | C4B—N3B—C2B | 119.34 (19) |
N7A—C4A—C5A | 123.7 (2) | C4B—N7B—H7B | 118 (2) |
N3A—C4A—C5A | 118.2 (2) | C4B—N7B—H8B | 119.6 (19) |
C6A—C5A—C4A | 118.1 (2) | H7B—N7B—H8B | 123 (3) |
C6A—C5A—H5A | 121.0 | C13—C12—C17 | 118.6 (3) |
C4A—C5A—H5A | 121.0 | C13—C12—C11 | 119.6 (2) |
C5A—C6A—N1A | 121.9 (2) | C17—C12—C11 | 121.8 (2) |
C5A—C6A—H6A | 119.1 | C14—C13—C12 | 121.9 (3) |
N1A—C6A—H6A | 119.1 | C14—C13—H13 | 119.1 |
C2A—N1A—C6A | 122.3 (2) | C12—C13—H13 | 119.1 |
C2A—N1A—H1A | 121 (2) | C13—C14—C15 | 117.9 (3) |
C6A—N1A—H1A | 117 (2) | C13—C14—H14 | 121.0 |
C4A—N3A—C2A | 123.6 (2) | C15—C14—H14 | 121.0 |
C4A—N3A—H3A | 121 (2) | C16—C15—C14 | 121.8 (3) |
C2A—N3A—H3A | 115 (2) | C16—C15—N18 | 119.8 (3) |
C4A—N7A—H7A | 120 (2) | C14—C15—N18 | 118.3 (3) |
C4A—N7A—H8A | 119.4 (16) | C15—C16—C17 | 119.5 (3) |
H7A—N7A—H8A | 121 (3) | C15—C16—H16 | 120.3 |
O8B—C2B—N1B | 119.4 (2) | C17—C16—H16 | 120.3 |
O8B—C2B—N3B | 121.5 (2) | C16—C17—C12 | 120.2 (3) |
N1B—C2B—N3B | 119.2 (2) | C16—C17—H17 | 119.9 |
N7B—C4B—N3B | 117.2 (2) | C12—C17—H17 | 119.9 |
N7B—C4B—C5B | 120.9 (2) | O9—C11—O10 | 124.9 (3) |
N3B—C4B—C5B | 121.8 (2) | O9—C11—C12 | 117.0 (3) |
C6B—C5B—C4B | 117.0 (2) | O10—C11—C12 | 118.0 (2) |
C6B—C5B—H5B | 121.5 | O19—N18—O20 | 123.8 (3) |
C4B—C5B—H5B | 121.5 | O19—N18—C15 | 118.6 (4) |
C5B—C6B—N1B | 120.7 (2) | O20—N18—C15 | 117.6 (4) |
C5B—C6B—H6B | 119.7 | H1W—O1W—H2W | 101 (3) |
N1B—C6B—H6B | 119.7 | | |
| | | |
N7A—C4A—C5A—C6A | 178.5 (2) | N1B—C2B—N3B—C4B | −1.1 (3) |
N3A—C4A—C5A—C6A | −0.9 (3) | C17—C12—C13—C14 | −1.5 (5) |
C4A—C5A—C6A—N1A | 0.2 (4) | C11—C12—C13—C14 | 177.0 (3) |
O8A—C2A—N1A—C6A | 178.9 (2) | C12—C13—C14—C15 | 1.0 (5) |
N3A—C2A—N1A—C6A | −1.4 (3) | C13—C14—C15—C16 | −0.1 (5) |
C5A—C6A—N1A—C2A | 1.0 (4) | C13—C14—C15—N18 | −180.0 (3) |
N7A—C4A—N3A—C2A | −179.0 (2) | C14—C15—C16—C17 | −0.3 (5) |
C5A—C4A—N3A—C2A | 0.5 (3) | N18—C15—C16—C17 | 179.5 (3) |
O8A—C2A—N3A—C4A | −179.7 (2) | C15—C16—C17—C12 | −0.2 (5) |
N1A—C2A—N3A—C4A | 0.7 (3) | C13—C12—C17—C16 | 1.1 (4) |
N7B—C4B—C5B—C6B | 178.3 (2) | C11—C12—C17—C16 | −177.4 (3) |
N3B—C4B—C5B—C6B | −2.3 (3) | C13—C12—C11—O9 | 1.5 (4) |
C4B—C5B—C6B—N1B | 0.8 (4) | C17—C12—C11—O9 | 180.0 (3) |
C5B—C6B—N1B—C2B | 0.5 (4) | C13—C12—C11—O10 | −176.1 (3) |
O8B—C2B—N1B—C6B | 179.9 (2) | C17—C12—C11—O10 | 2.3 (4) |
N3B—C2B—N1B—C6B | −0.3 (3) | C16—C15—N18—O19 | 176.4 (3) |
N7B—C4B—N3B—C2B | −178.1 (2) | C14—C15—N18—O19 | −3.7 (5) |
C5B—C4B—N3B—C2B | 2.4 (3) | C16—C15—N18—O20 | −4.0 (5) |
O8B—C2B—N3B—C4B | 178.66 (19) | C14—C15—N18—O20 | 175.9 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1A—H1A···O1W | 0.91 (4) | 1.80 (4) | 2.710 (3) | 173 (3) |
N3A—H3A···N3B | 0.97 (4) | 1.88 (4) | 2.846 (3) | 177 (3) |
N7A—H7A···O8Ai | 0.85 (3) | 2.11 (3) | 2.900 (3) | 154 (3) |
N7A—H8A···O8B | 0.98 (3) | 1.76 (3) | 2.747 (3) | 175 (2) |
N1B—H1B···O10 | 0.85 (4) | 1.90 (4) | 2.731 (3) | 169 (3) |
N7B—H7B···O8Bii | 0.86 (4) | 2.18 (4) | 2.889 (3) | 139 (3) |
N7B—H8B···O8A | 0.89 (3) | 2.06 (3) | 2.949 (3) | 174 (3) |
O1W—H1W···O10iii | 0.92 (3) | 1.97 (3) | 2.847 (3) | 159 (3) |
O1W—H2W···O9iv | 0.85 (5) | 1.87 (5) | 2.723 (3) | 175 (4) |
C5B—H5B···O10ii | 0.93 | 2.32 | 3.249 (3) | 176 |
C6A—H6A···O19v | 0.93 | 2.38 | 3.262 (4) | 159 |
Symmetry codes: (i) x, y−1, z; (ii) x, y+1, z; (iii) −x+1, −y, −z+1; (iv) −x+2, −y, −z+1; (v) x, y+1, z−1. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C4H6N3O+·C4H5O4− | C4H6N3O+·C7H4NO4−·C4H5N3O·H2O |
Mr | 229.20 | 407.36 |
Crystal system, space group | Monoclinic, C2/c | Triclinic, P1 |
Temperature (K) | 294 | 294 |
a, b, c (Å) | 15.666 (3), 6.6959 (9), 18.726 (3) | 6.7154 (14), 7.4036 (16), 19.228 (4) |
α, β, γ (°) | 90, 100.480 (4), 90 | 85.525 (4), 87.576 (4), 67.279 (3) |
V (Å3) | 1931.5 (5) | 879.0 (3) |
Z | 8 | 2 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.13 | 0.13 |
Crystal size (mm) | 0.23 × 0.17 × 0.13 | 0.19 × 0.16 × 0.08 |
|
Data collection |
Diffractometer | Bruker SMART APEX CCD area-detector diffractometer | Bruker SMART APEX CCD area-detector diffractometer |
Absorption correction | – | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8824, 1697, 1607 | 8258, 3064, 2570 |
Rint | 0.021 | 0.044 |
(sin θ/λ)max (Å−1) | 0.595 | 0.595 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.108, 1.10 | 0.070, 0.209, 1.10 |
No. of reflections | 1697 | 3064 |
No. of parameters | 165 | 298 |
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) | 0.22, −0.19 | 0.43, −0.45 |
Selected geometric parameters (Å, º) for (I) topC11—O9 | 1.2468 (18) | C11—C12 | 1.5141 (19) |
C11—O10 | 1.2653 (19) | C13—C14 | 1.4993 (19) |
| | | |
C11—C12—C13—C14 | 179.41 (11) | | |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O15i | 0.88 (2) | 2.02 (2) | 2.9018 (18) | 175 (2) |
N3—H3N···O9 | 0.95 (2) | 1.65 (2) | 2.5916 (15) | 172 (2) |
N7—H7N···O10 | 0.91 (2) | 2.08 (2) | 2.9854 (18) | 171.0 (17) |
N7—H8N···O8ii | 0.89 (3) | 2.00 (2) | 2.8122 (19) | 150.5 (19) |
O16—H16O···O10iii | 1.01 (3) | 1.51 (3) | 2.5250 (16) | 176 (2) |
C5—H5···O8ii | 0.93 | 2.24 | 2.970 (2) | 135 |
Symmetry codes: (i) x−1/2, −y+5/2, z−1/2; (ii) x, y−1, z; (iii) x, y+1, z. |
Selected bond lengths (Å) for (II) topC11—O9 | 1.235 (4) | C11—O10 | 1.248 (3) |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1A—H1A···O1W | 0.91 (4) | 1.80 (4) | 2.710 (3) | 173 (3) |
N3A—H3A···N3B | 0.97 (4) | 1.88 (4) | 2.846 (3) | 177 (3) |
N7A—H7A···O8Ai | 0.85 (3) | 2.11 (3) | 2.900 (3) | 154 (3) |
N7A—H8A···O8B | 0.98 (3) | 1.76 (3) | 2.747 (3) | 175 (2) |
N1B—H1B···O10 | 0.85 (4) | 1.90 (4) | 2.731 (3) | 169 (3) |
N7B—H7B···O8Bii | 0.86 (4) | 2.18 (4) | 2.889 (3) | 139 (3) |
N7B—H8B···O8A | 0.89 (3) | 2.06 (3) | 2.949 (3) | 174 (3) |
O1W—H1W···O10iii | 0.92 (3) | 1.97 (3) | 2.847 (3) | 159 (3) |
O1W—H2W···O9iv | 0.85 (5) | 1.87 (5) | 2.723 (3) | 175 (4) |
C5B—H5B···O10ii | 0.93 | 2.32 | 3.249 (3) | 176 |
C6A—H6A···O19v | 0.93 | 2.38 | 3.262 (4) | 159 |
Symmetry codes: (i) x, y−1, z; (ii) x, y+1, z; (iii) −x+1, −y, −z+1; (iv) −x+2, −y, −z+1; (v) x, y+1, z−1. |
The protonated cytosine–cytosine base pair carries important structural implications for biological systems. In particular, this base pair is known to self-assemble in acidic media (Armentano et al., 2004) and is also found in RNA and DNA solutions. Furthermore, X-ray studies have revealed that the cytosine–cytosine base pair contributes to fully intercalated parallel-stranded duplexes of DNA structural motifs in crystals (Kang et al., 1994; Kang et al., 1995). Carboxylic acids belong to an important class of organic molecules and are believed to have existed in the prebiotic earth (Miller & Orgel, 1974; Kvenvolden et al., 1971). Succinic acid may bind to cations in either the monoanionic or the dianionic form, displaying a plethora of interesting structures. Succinic acid, with two carboxyl functions, can exist as a neutral molecule or as single negatively charged or double negatively charged ions (Prasad & Vijayan, 1991). 4-Nitrobenzoic acid can easily lose its acidic H atom and form complexes with other compounds through hydrogen bonding. The present study is a continuation of our ongoing programme on structure elucidation of nucleobases with the carboxylic and aromatic acids.
In the structures of (I) and (II), the bond lengths and angles (Table 1 and 3) correspond to those expected for the atom types and the type of hybridization (Allen et al., 1987). The asymmetric unit of (I) contains one cytosinium cation protonated at atom N3 and one succinate anion, with one of the carboxyl group deprotonated (Fig. 1), while (II) comprises one cytosinium cation (A), one cytosine molecule (B), one 4-nitrobenzoate anion and one water molecule (Fig. 2). As expected, both the succinate and the 4-nitrobenzoate anions of (I) and (II) are planar. In the succinate anion of (I), the two Csp2—Csp2 single-bond distances of the carboxylate (C11—C12) and carboxyl (C13—C14) groups are not identical (Table 1). It is of interest to note that the shorter C13—C14 bond links the carboxyl group, while the longer C11—C12 bond links the carboxylate group. The C11—C12—C13—C14 unit is in a trans conformation in (I) (Table 1). In the 4-nitrobenzoate anion of (II), the mean planes of the carboxylate group (C11/O9/O10) and nitro group (N18/O19/O20) make dihedral angles of 1.9 (3) and 3.8 (2)°, respectively, with respect to the mean plane of the benzene ring (C12–C17). In (I), the O—H bond of the carboxyl group is in a trans conformation with respect to the C═O bond, as evidenced from the H16O—O16—C114—O15 torsion angle of 176.9 (6)°.
Cytosine is a quite strong base (pKa1 = 1. 6 and pKa2 = 12.2; Stecher, 1968) and, in the presence of acids, is readily protonated at the N3 ring position. The molecular geometries of the cytosine and cytosinium cation are in good agreement with those of similar structures (Görbitz & Sagstuen, 2004; Garcia-Teran et al., 2007). The N3 protonation or its absence reflects in the C2—N3—C4 bond angle. The N3 protonation of the cytosine ring is consistent with the larger C2—N3—C4 bond angle [124.0 (1)° in (I) and 123.6 (2)° in molecule A of (II)], while for unprotonated cytosine the angle is 119.3 (2)°, which agrees well with the reported value of the unprotonated cytosine molecule of 119.4° (McClure & Craven, 1973).
In (I), the cytosinium cation and succinate anion are held together by two N—H···O hydrogen bonds (Table 2), thereby generating an R22(8) motif (Bernstein et al., 1995), which is further interconnected by intermolecular N—H···O and O—H···O interactions involving the the cytosinium cations and succinate anions leading to the formation of a two-dimensional sheet containing R44(15) and R44(19) motifs (Fig. 3). In the case of (II), the cytosinium–cytosine dimers are formed by two N—H···O and one N—H···N hydrogen bonds (Table 4), thus resembling a pseudo-Watson–Crick pattern. Furthermore, adjacent cytosinium–cytosine base pairs are interlinked by double N—H···O hydrogen bonds (Table 4), leading to one-dimensional supramolecular polymeric ribbons with alternating neutral and protonated cytosine entities (Fig. 4).
In (II), atom N1 of the cytosinium cation forms an N—H···O hydrogen bond with the water molecule, while the corresponding atom of the cytosine molecule forms an N—H···O hydrogen bond with the 4-nitrobenzoate anion. The water molecule plays a dual role as both donor and acceptor in the hydrogen-bonding interactions (Table 4). It is involved in three hydrogen bonds, acting donor to two inversion-related 4-nitrobenzoate anions and acceptor to an adjacent cytosinium cation.
In (II), the combination of N—H···O, N—H···N and O—H···O hydrogen bonds involving the cytosinium–cytosine base pairs, the 4-nitrobnzoate anions and the water molecules leads to two-dimensional hydrogen-bonded network cavities, which extend parallel to the c axis. Each cavity is arranged like a hexamer hydrogen-bonded network consisting of two sets of parallel cytosinium–cytosine base pairs, which are sandwiched between the two 4-nitrobenzoate anions and two water molecules (Fig. 5). The one-dimension polymeric ribbon formed by the cytosinium–cytosine base pair interacts with adjacent ribbons through 4-nitrobenzoate anions and water molecules via N—H···O and O—H···O hydrogen bonds, thereby generating a two-dimensional supramolecular hydrogen-bonded network in the crystal structure. It is very interesting to note that the nitro group of the 4-nitrobenzoate anion does not participate in any conventional hydrogen-bonding interactions. In (II), the water molecule does not have any interaction with the cytosine molecule, while the 4-nitrobenzate anion links the cytosinium cation through a weak C—H···O interaction.