The asymmetric unit of the title compound [systematic name: 4-amino-2-oxo-2,3-dihydropyrimidin-1-ium 1-hydroxy-2-(1
H,3
H-imidazol-3-ium-1-yl)ethylidenediphosphonate trihydrate], C
4H
6N
3O
+·C
5H
9N
2O
7P
2−·3H
2O, contains one cytosinium cation, one zoledronate anion and three water molecules. The zoledronate anion has a zwitterionic character, in which each phosphonate group is singly deprotonated and an imidazole N atom is protonated. Furthermore, proton transfer takes place from one of the phosphonic acid groups of the zoledronate anion to one of the N atoms of the cytosinium cation. The cytosinium cation forms a
C(6) chain, while the zoledronate anion forms a rectangular-shaped centrosymmetric dimer through N—H
O hydrogen bonds. The cations and anions are held together by N—H
O and O—H
O hydrogen bonds to form a one-dimensional polymeric tape. The three water molecules play a crucial role in hydrogen bonding, resulting in a three-dimensional hydrogen-bonded network.
Supporting information
CCDC reference: 819308
To obtain crystals of (I) suitable for X-ray study, cytosine (0.111 g, 1 mmol)
and zoledronic acid (USV Ltd, Mumbai; 0.272 g, 1 mmol) were dissolved in water
(25 ml) and the solution was allowed to evaporate slowly.
All H atoms attached to C, N and hydroxyl O atoms were fixed geometrically and
treated as riding, with C—H = 0.93 (aromatic) or 0.97 Å (methylene), N—H
= 0.86 Å and O—H = 0.82 Å, with Uiso(H) = 1.2Ueq(C,N)
or 1.5Ueq(O). Water H atoms were located in a difference Fourier map
and included in the subsequent refinement using restraints O—H = 0.85 (1) Å
and H···H = 1.40 (2) Å, with Uiso(H) = 1.5Ueq(O). In the
last cycle of refinement, they were treated as riding on their parent O atoms.
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: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).
4-amino-2-oxo- 2,3-dihydropyrimidin-1-ium
1-hydroxy-2-(1
H,3
H-imidazol-3-ium-1-yl)ethylidenediphosphonate
trihydrate
top
Crystal data top
C4H6N3O+·C5H9N2O7P2−·3H2O | Z = 2 |
Mr = 437.25 | F(000) = 456 |
Triclinic, P1 | Dx = 1.662 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.7292 (16) Å | Cell parameters from 4828 reflections |
b = 6.8032 (16) Å | θ = 3.0–27.9° |
c = 19.193 (5) Å | µ = 0.32 mm−1 |
α = 89.875 (4)° | T = 294 K |
β = 86.747 (5)° | Block, colourless |
γ = 84.726 (4)° | 0.14 × 0.12 × 0.06 mm |
V = 873.5 (4) Å3 | |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 2805 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.033 |
Graphite monochromator | θmax = 25.0°, θmin = 1.1° |
ω scans | h = −7→7 |
7859 measured reflections | k = −8→8 |
3035 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)] = 0.060 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.143 | H-atom parameters constrained |
S = 1.21 | w = 1/[σ2(Fo2) + (0.0511P)2 + 1.5176P] where P = (Fo2 + 2Fc2)/3 |
3035 reflections | (Δ/σ)max < 0.001 |
247 parameters | Δρmax = 0.50 e Å−3 |
9 restraints | Δρmin = −0.38 e Å−3 |
Crystal data top
C4H6N3O+·C5H9N2O7P2−·3H2O | γ = 84.726 (4)° |
Mr = 437.25 | V = 873.5 (4) Å3 |
Triclinic, P1 | Z = 2 |
a = 6.7292 (16) Å | Mo Kα radiation |
b = 6.8032 (16) Å | µ = 0.32 mm−1 |
c = 19.193 (5) Å | T = 294 K |
α = 89.875 (4)° | 0.14 × 0.12 × 0.06 mm |
β = 86.747 (5)° | |
Data collection top
Bruker SMART APEX CCD area-detector diffractometer | 2805 reflections with I > 2σ(I) |
7859 measured reflections | Rint = 0.033 |
3035 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.060 | 9 restraints |
wR(F2) = 0.143 | H-atom parameters constrained |
S = 1.21 | Δρmax = 0.50 e Å−3 |
3035 reflections | Δρmin = −0.38 e Å−3 |
247 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 | |
P1 | 0.94429 (14) | 0.03787 (12) | 0.20340 (5) | 0.0218 (2) | |
P2 | 0.66606 (14) | 0.41161 (12) | 0.24243 (5) | 0.0225 (2) | |
O16 | 0.8769 (4) | 0.3519 (4) | 0.11825 (12) | 0.0278 (6) | |
H16 | 0.9828 | 0.3828 | 0.1321 | 0.042* | |
O17 | 1.0732 (4) | −0.0474 (4) | 0.14326 (13) | 0.0335 (6) | |
O18 | 0.8167 (4) | −0.1022 (3) | 0.24127 (13) | 0.0320 (6) | |
O19 | 1.0732 (4) | 0.1384 (4) | 0.25599 (15) | 0.0380 (7) | |
H19 | 1.1796 | 0.0710 | 0.2595 | 0.057* | |
O20 | 0.5988 (4) | 0.2830 (4) | 0.30150 (12) | 0.0294 (6) | |
O21 | 0.5096 (4) | 0.5515 (4) | 0.21253 (13) | 0.0325 (6) | |
O22 | 0.8447 (4) | 0.5239 (4) | 0.26582 (14) | 0.0322 (6) | |
H22 | 0.8358 | 0.6359 | 0.2497 | 0.048* | |
N9 | 0.6674 (4) | 0.0276 (4) | 0.07833 (14) | 0.0232 (6) | |
N11 | 0.7866 (5) | −0.0766 (5) | −0.02246 (16) | 0.0336 (8) | |
H11 | 0.8330 | −0.0779 | −0.0652 | 0.040* | |
C10 | 0.7323 (5) | 0.0811 (5) | 0.01536 (18) | 0.0267 (8) | |
H10 | 0.7384 | 0.2106 | 0.0003 | 0.032* | |
C12 | 0.7567 (6) | −0.2397 (6) | 0.0177 (2) | 0.0363 (9) | |
H12 | 0.7838 | −0.3707 | 0.0038 | 0.044* | |
C13 | 0.6813 (6) | −0.1757 (5) | 0.0807 (2) | 0.0321 (9) | |
H13 | 0.6456 | −0.2533 | 0.1185 | 0.038* | |
C14 | 0.6019 (5) | 0.1652 (5) | 0.13577 (18) | 0.0255 (8) | |
H14A | 0.5214 | 0.0984 | 0.1702 | 0.031* | |
H14B | 0.5183 | 0.2753 | 0.1178 | 0.031* | |
C15 | 0.7772 (5) | 0.2448 (5) | 0.17136 (17) | 0.0207 (7) | |
O8 | 0.7341 (6) | 0.5225 (4) | 0.45878 (17) | 0.0607 (10) | |
N1 | 0.7579 (5) | 0.2882 (5) | 0.54241 (16) | 0.0346 (8) | |
H1 | 0.7661 | 0.3746 | 0.5745 | 0.042* | |
N3 | 0.7418 (5) | 0.2030 (4) | 0.42667 (16) | 0.0301 (7) | |
H3 | 0.7318 | 0.2373 | 0.3838 | 0.036* | |
N7 | 0.7618 (5) | −0.1186 (4) | 0.39070 (16) | 0.0338 (8) | |
H7A | 0.7596 | −0.0775 | 0.3483 | 0.041* | |
H7B | 0.7694 | −0.2431 | 0.3993 | 0.041* | |
C2 | 0.7446 (7) | 0.3486 (6) | 0.4753 (2) | 0.0360 (9) | |
C4 | 0.7537 (5) | 0.0073 (5) | 0.44174 (18) | 0.0248 (8) | |
C5 | 0.7559 (6) | −0.0465 (5) | 0.51256 (19) | 0.0281 (8) | |
H5 | 0.7555 | −0.1782 | 0.5257 | 0.034* | |
C6 | 0.7585 (6) | 0.0940 (6) | 0.56041 (19) | 0.0307 (8) | |
H6 | 0.7608 | 0.0592 | 0.6073 | 0.037* | |
O1W | 0.3927 (4) | 0.9094 (4) | 0.27836 (14) | 0.0362 (7) | |
H1W | 0.5046 | 0.9575 | 0.2789 | 0.054* | |
H2W | 0.4060 | 0.7998 | 0.2573 | 0.054* | |
O2W | 0.1989 (4) | 0.5602 (4) | 0.12357 (16) | 0.0410 (7) | |
H3W | 0.2902 | 0.5443 | 0.1528 | 0.061* | |
H4W | 0.1487 | 0.6796 | 0.1250 | 0.061* | |
O3W | 0.7872 (5) | 0.5746 (5) | 0.64102 (16) | 0.0522 (8) | |
H5W | 0.6780 | 0.6194 | 0.6623 | 0.078* | |
H6W | 0.8848 | 0.5786 | 0.6669 | 0.078* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
P1 | 0.0307 (5) | 0.0110 (4) | 0.0236 (5) | 0.0004 (3) | −0.0052 (4) | 0.0008 (3) |
P2 | 0.0317 (5) | 0.0130 (4) | 0.0226 (5) | 0.0015 (4) | −0.0062 (4) | 0.0008 (3) |
O16 | 0.0360 (15) | 0.0218 (13) | 0.0273 (13) | −0.0096 (11) | −0.0046 (11) | 0.0061 (10) |
O17 | 0.0447 (17) | 0.0205 (13) | 0.0341 (15) | 0.0044 (12) | −0.0028 (12) | 0.0018 (11) |
O18 | 0.0464 (16) | 0.0131 (12) | 0.0359 (14) | −0.0013 (11) | 0.0010 (12) | 0.0046 (10) |
O19 | 0.0409 (17) | 0.0250 (14) | 0.0483 (17) | 0.0089 (12) | −0.0216 (13) | −0.0087 (12) |
O20 | 0.0422 (16) | 0.0219 (13) | 0.0240 (13) | −0.0026 (11) | −0.0004 (11) | 0.0017 (10) |
O21 | 0.0391 (15) | 0.0230 (13) | 0.0344 (14) | 0.0074 (11) | −0.0101 (12) | 0.0018 (11) |
O22 | 0.0441 (16) | 0.0138 (12) | 0.0396 (15) | −0.0005 (11) | −0.0133 (12) | 0.0007 (11) |
N9 | 0.0306 (16) | 0.0179 (14) | 0.0222 (15) | −0.0045 (12) | −0.0072 (12) | −0.0010 (11) |
N11 | 0.0370 (19) | 0.0389 (19) | 0.0256 (16) | −0.0072 (15) | −0.0031 (14) | −0.0062 (14) |
C10 | 0.032 (2) | 0.0252 (19) | 0.0241 (18) | −0.0066 (15) | −0.0069 (15) | 0.0016 (15) |
C12 | 0.042 (2) | 0.023 (2) | 0.045 (2) | −0.0009 (17) | −0.0117 (19) | −0.0075 (17) |
C13 | 0.045 (2) | 0.0197 (18) | 0.033 (2) | −0.0061 (16) | −0.0123 (17) | 0.0055 (16) |
C14 | 0.031 (2) | 0.0224 (18) | 0.0235 (18) | −0.0019 (15) | −0.0057 (15) | −0.0014 (14) |
C15 | 0.0275 (18) | 0.0113 (15) | 0.0233 (17) | −0.0011 (13) | −0.0031 (14) | 0.0024 (13) |
O8 | 0.121 (3) | 0.0168 (15) | 0.0457 (18) | −0.0088 (17) | −0.0110 (19) | 0.0054 (13) |
N1 | 0.054 (2) | 0.0213 (16) | 0.0285 (17) | −0.0027 (15) | −0.0062 (15) | −0.0064 (13) |
N3 | 0.050 (2) | 0.0169 (15) | 0.0237 (15) | −0.0038 (14) | −0.0061 (14) | 0.0027 (12) |
N7 | 0.059 (2) | 0.0167 (15) | 0.0263 (16) | −0.0038 (14) | −0.0053 (15) | 0.0033 (13) |
C2 | 0.055 (3) | 0.0192 (19) | 0.034 (2) | −0.0023 (17) | −0.0057 (19) | 0.0008 (16) |
C4 | 0.0287 (19) | 0.0189 (17) | 0.0273 (18) | −0.0033 (14) | −0.0035 (15) | 0.0038 (14) |
C5 | 0.035 (2) | 0.0195 (18) | 0.0301 (19) | −0.0042 (15) | −0.0023 (16) | 0.0047 (15) |
C6 | 0.036 (2) | 0.030 (2) | 0.0251 (19) | −0.0018 (16) | −0.0005 (16) | 0.0050 (16) |
O1W | 0.0326 (15) | 0.0333 (15) | 0.0418 (16) | 0.0031 (12) | −0.0050 (12) | −0.0022 (12) |
O2W | 0.0447 (17) | 0.0224 (14) | 0.0570 (18) | −0.0013 (12) | −0.0167 (14) | −0.0046 (13) |
O3W | 0.053 (2) | 0.058 (2) | 0.0469 (18) | −0.0094 (16) | 0.0010 (15) | −0.0255 (16) |
Geometric parameters (Å, º) top
P1—O17 | 1.489 (3) | C14—H14A | 0.9700 |
P1—O18 | 1.500 (3) | C14—H14B | 0.9700 |
P1—O19 | 1.566 (3) | O8—C2 | 1.221 (5) |
P1—C15 | 1.846 (3) | N1—C2 | 1.356 (5) |
P2—O21 | 1.492 (3) | N1—C6 | 1.364 (5) |
P2—O20 | 1.505 (3) | N1—H1 | 0.8600 |
P2—O22 | 1.569 (3) | N3—C4 | 1.358 (5) |
P2—C15 | 1.856 (3) | N3—C2 | 1.365 (5) |
O16—C15 | 1.425 (4) | N3—H3 | 0.8600 |
O16—H16 | 0.8200 | N7—C4 | 1.298 (5) |
O19—H19 | 0.8200 | N7—H7A | 0.8600 |
O22—H22 | 0.8200 | N7—H7B | 0.8600 |
N9—C10 | 1.324 (4) | C4—C5 | 1.407 (5) |
N9—C13 | 1.378 (5) | C5—C6 | 1.329 (5) |
N9—C14 | 1.470 (4) | C5—H5 | 0.9300 |
N11—C10 | 1.309 (5) | C6—H6 | 0.9300 |
N11—C12 | 1.373 (5) | O1W—H1W | 0.8492 |
N11—H11 | 0.8600 | O1W—H2W | 0.8447 |
C10—H10 | 0.9300 | O2W—H3W | 0.8548 |
C12—C13 | 1.342 (6) | O2W—H4W | 0.8501 |
C12—H12 | 0.9300 | O3W—H5W | 0.8516 |
C13—H13 | 0.9300 | O3W—H6W | 0.8488 |
C14—C15 | 1.537 (5) | | |
| | | |
O17—P1—O18 | 115.68 (15) | N9—C14—H14B | 109.0 |
O17—P1—O19 | 110.34 (16) | C15—C14—H14B | 109.0 |
O18—P1—O19 | 110.12 (16) | H14A—C14—H14B | 107.8 |
O17—P1—C15 | 108.43 (15) | O16—C15—C14 | 104.8 (3) |
O18—P1—C15 | 107.85 (15) | O16—C15—P1 | 111.1 (2) |
O19—P1—C15 | 103.69 (15) | C14—C15—P1 | 110.0 (2) |
O21—P2—O20 | 116.77 (16) | O16—C15—P2 | 111.1 (2) |
O21—P2—O22 | 110.79 (15) | C14—C15—P2 | 106.6 (2) |
O20—P2—O22 | 108.90 (15) | P1—C15—P2 | 112.80 (17) |
O21—P2—C15 | 107.97 (15) | C2—N1—C6 | 121.8 (3) |
O20—P2—C15 | 107.11 (14) | C2—N1—H1 | 119.1 |
O22—P2—C15 | 104.53 (15) | C6—N1—H1 | 119.1 |
C15—O16—H16 | 109.5 | C4—N3—C2 | 124.1 (3) |
P1—O19—H19 | 109.5 | C4—N3—H3 | 117.9 |
P2—O22—H22 | 109.5 | C2—N3—H3 | 117.9 |
C10—N9—C13 | 108.3 (3) | C4—N7—H7A | 120.0 |
C10—N9—C14 | 124.6 (3) | C4—N7—H7B | 120.0 |
C13—N9—C14 | 127.0 (3) | H7A—N7—H7B | 120.0 |
C10—N11—C12 | 108.3 (3) | O8—C2—N1 | 122.6 (4) |
C10—N11—H11 | 125.9 | O8—C2—N3 | 121.4 (4) |
C12—N11—H11 | 125.9 | N1—C2—N3 | 116.0 (3) |
N11—C10—N9 | 109.4 (3) | N7—C4—N3 | 118.7 (3) |
N11—C10—H10 | 125.3 | N7—C4—C5 | 123.9 (3) |
N9—C10—H10 | 125.3 | N3—C4—C5 | 117.4 (3) |
C13—C12—N11 | 107.6 (3) | C6—C5—C4 | 118.9 (3) |
C13—C12—H12 | 126.2 | C6—C5—H5 | 120.6 |
N11—C12—H12 | 126.2 | C4—C5—H5 | 120.6 |
C12—C13—N9 | 106.5 (3) | C5—C6—N1 | 121.5 (3) |
C12—C13—H13 | 126.8 | C5—C6—H6 | 119.2 |
N9—C13—H13 | 126.8 | N1—C6—H6 | 119.2 |
N9—C14—C15 | 112.9 (3) | H1W—O1W—H2W | 110.1 |
N9—C14—H14A | 109.0 | H3W—O2W—H4W | 109.2 |
C15—C14—H14A | 109.0 | H5W—O3W—H6W | 111.1 |
| | | |
C12—N11—C10—N9 | −0.3 (4) | O19—P1—C15—P2 | −44.9 (2) |
C13—N9—C10—N11 | 0.0 (4) | O21—P2—C15—O16 | 63.8 (3) |
C14—N9—C10—N11 | 177.4 (3) | O20—P2—C15—O16 | −169.7 (2) |
C10—N11—C12—C13 | 0.5 (4) | O22—P2—C15—O16 | −54.2 (3) |
N11—C12—C13—N9 | −0.4 (4) | O21—P2—C15—C14 | −49.8 (3) |
C10—N9—C13—C12 | 0.3 (4) | O20—P2—C15—C14 | 76.7 (2) |
C14—N9—C13—C12 | −177.0 (3) | O22—P2—C15—C14 | −167.8 (2) |
C10—N9—C14—C15 | −77.6 (4) | O21—P2—C15—P1 | −170.67 (17) |
C13—N9—C14—C15 | 99.3 (4) | O20—P2—C15—P1 | −44.1 (2) |
N9—C14—C15—O16 | 62.9 (3) | O22—P2—C15—P1 | 71.3 (2) |
N9—C14—C15—P1 | −56.7 (3) | C6—N1—C2—O8 | 176.3 (4) |
N9—C14—C15—P2 | −179.3 (2) | C6—N1—C2—N3 | −3.1 (6) |
O17—P1—C15—O16 | −36.7 (3) | C4—N3—C2—O8 | 179.8 (4) |
O18—P1—C15—O16 | −162.7 (2) | C4—N3—C2—N1 | −0.8 (6) |
O19—P1—C15—O16 | 80.6 (2) | C2—N3—C4—N7 | −175.9 (4) |
O17—P1—C15—C14 | 78.9 (3) | C2—N3—C4—C5 | 4.3 (6) |
O18—P1—C15—C14 | −47.0 (3) | N7—C4—C5—C6 | 176.2 (4) |
O19—P1—C15—C14 | −163.8 (2) | N3—C4—C5—C6 | −4.0 (5) |
O17—P1—C15—P2 | −162.17 (17) | C4—C5—C6—N1 | 0.4 (6) |
O18—P1—C15—P2 | 71.9 (2) | C2—N1—C6—C5 | 3.3 (6) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O3W | 0.86 | 1.89 | 2.747 (4) | 177 |
N3—H3···O20 | 0.86 | 1.87 | 2.675 (4) | 155 |
N7—H7A···O18 | 0.86 | 2.07 | 2.874 (4) | 155 |
N7—H7B···O8i | 0.86 | 1.98 | 2.783 (4) | 154 |
O16—H16···O2Wii | 0.82 | 1.97 | 2.703 (4) | 148 |
O19—H19···O1Wiii | 0.82 | 1.78 | 2.592 (4) | 172 |
O22—H22···O18iv | 0.82 | 1.78 | 2.578 (3) | 163 |
N11—H11···O17v | 0.86 | 1.83 | 2.620 (4) | 152 |
O1W—H1W···O18iv | 0.85 | 2.18 | 2.895 (4) | 141 |
O1W—H1W···O20iv | 0.85 | 2.41 | 3.050 (4) | 133 |
O1W—H2W···O21 | 0.84 | 1.95 | 2.774 (4) | 165 |
O2W—H3W···O21 | 0.85 | 1.92 | 2.770 (4) | 170 |
O2W—H4W···O17vi | 0.85 | 1.91 | 2.746 (4) | 168 |
O3W—H5W···O20vii | 0.85 | 2.01 | 2.849 (4) | 171 |
O3W—H6W···O22viii | 0.85 | 2.34 | 3.158 (4) | 161 |
O3W—H6W···O19viii | 0.85 | 2.48 | 3.027 (4) | 123 |
C5—H5···O8i | 0.93 | 2.43 | 3.130 (5) | 132 |
C6—H6···O1Wvii | 0.93 | 2.37 | 3.203 (5) | 148 |
C13—H13···O21i | 0.93 | 2.43 | 3.350 (5) | 173 |
C14—H14A···O1Wi | 0.97 | 2.59 | 3.534 (5) | 165 |
Symmetry codes: (i) x, y−1, z; (ii) x+1, y, z; (iii) x+1, y−1, z; (iv) x, y+1, z; (v) −x+2, −y, −z; (vi) x−1, y+1, z; (vii) −x+1, −y+1, −z+1; (viii) −x+2, −y+1, −z+1. |
Experimental details
Crystal data |
Chemical formula | C4H6N3O+·C5H9N2O7P2−·3H2O |
Mr | 437.25 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 294 |
a, b, c (Å) | 6.7292 (16), 6.8032 (16), 19.193 (5) |
α, β, γ (°) | 89.875 (4), 86.747 (5), 84.726 (4) |
V (Å3) | 873.5 (4) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.32 |
Crystal size (mm) | 0.14 × 0.12 × 0.06 |
|
Data collection |
Diffractometer | Bruker SMART APEX CCD area-detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7859, 3035, 2805 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.595 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.060, 0.143, 1.21 |
No. of reflections | 3035 |
No. of parameters | 247 |
No. of restraints | 9 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.50, −0.38 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O3W | 0.86 | 1.89 | 2.747 (4) | 177 |
N3—H3···O20 | 0.86 | 1.87 | 2.675 (4) | 155 |
N7—H7A···O18 | 0.86 | 2.07 | 2.874 (4) | 155 |
N7—H7B···O8i | 0.86 | 1.98 | 2.783 (4) | 154 |
O16—H16···O2Wii | 0.82 | 1.97 | 2.703 (4) | 148 |
O19—H19···O1Wiii | 0.82 | 1.78 | 2.592 (4) | 172 |
O22—H22···O18iv | 0.82 | 1.78 | 2.578 (3) | 163 |
N11—H11···O17v | 0.86 | 1.83 | 2.620 (4) | 152 |
O1W—H1W···O18iv | 0.85 | 2.18 | 2.895 (4) | 141 |
O1W—H1W···O20iv | 0.85 | 2.41 | 3.050 (4) | 133 |
O1W—H2W···O21 | 0.84 | 1.95 | 2.774 (4) | 165 |
O2W—H3W···O21 | 0.85 | 1.92 | 2.770 (4) | 170 |
O2W—H4W···O17vi | 0.85 | 1.91 | 2.746 (4) | 168 |
O3W—H5W···O20vii | 0.85 | 2.01 | 2.849 (4) | 171 |
O3W—H6W···O22viii | 0.85 | 2.34 | 3.158 (4) | 161 |
O3W—H6W···O19viii | 0.85 | 2.48 | 3.027 (4) | 123 |
C5—H5···O8i | 0.93 | 2.43 | 3.130 (5) | 132 |
C6—H6···O1Wvii | 0.93 | 2.37 | 3.203 (5) | 148 |
C13—H13···O21i | 0.93 | 2.43 | 3.350 (5) | 173 |
C14—H14A···O1Wi | 0.97 | 2.59 | 3.534 (5) | 165 |
Symmetry codes: (i) x, y−1, z; (ii) x+1, y, z; (iii) x+1, y−1, z; (iv) x, y+1, z; (v) −x+2, −y, −z; (vi) x−1, y+1, z; (vii) −x+1, −y+1, −z+1; (viii) −x+2, −y+1, −z+1. |
Selected bond distances (Å), bond angles (°) and torsion angles (°)
for zoledronate complexes. topParameter | (I) | 1 | 2mole1 | 2mole 2 | 3 | 4 | 5 | 6mole 1 | 6mole2 |
P1-O17 | 1.489 (3) | 1.512 (2) | 1.517 (2) | 1.516 (2) | 1.501 (4) | 1.508 (2) | 1.503 (1) | 1.498 (4) | 1.497 (3) |
P1-O18 | 1.500 (3) | 1.503 (2) | 1.519 (2) | 1.504 (2) | 1.509 (4) | 1.508 (2) | 1.508 (1) | 1.522 (3) | 1.530 (3) |
P1-O19 | 1.566 (3) | 1.59 (2) | 1.567 (2) | 1.564 (2) | 1.567 (4) | 1.580 (2) | 1.557 (1) | 1.579 (3) | 1.574 (4) |
P2-O20 | 1.505 (3) | 1.501 (2) | 1.499 (2) | 1.505 (2) | 1.498 (4) | 1.506 (2) | 1.503 (1) | 1.482 (4) | 1.498 (4) |
P2-O21 | 1.492 (3) | 1.522 (2)* | 1.538 (2)* | 1.537 (2)* | 1.502 (4) | 1.497 (2) | 1.512 (1) | 1.521 (4) | 1.510 (4) |
P2-O22 | 1.569 (2) | 1.563 (2) | 1.553 (2) | 1.561 (2) | 1.578 (4) | 1.569 (2) | 1.566 (1) | 1.594 (4) | 1.581 (4) |
| | | | | | | | | |
O17-P1-O18 | 115.68 (15) | 116.0 (1) | 113.6 (1) | 116.1 (1) | 108.9 (2) | 115.4 (1) | 113.96 (9) | 115.5 (2) | 113.4 (2) |
O17-P1-O19 | 110.34 (16) | 112.25 (9) | 112.2 (1) | 105.0 (1) | 115.5 (2) | 108.1 (1) | 110.93 (9) | 110.2 (2) | 110.5 (2) |
O18-P1-O19 | 110.12 (16) | 107.7 (1) | 110.0 (1) | 114.8 (1) | 109.9 (2) | 110.5 (1) | 111.03 (8) | 108.1 (2) | 107.7 (2) |
O21-P2-O20 | 116.77 (16) | 109.1 (1)$ | 114.3 (1)$ | 110.9 (1)$ | 108.0 (3) | 110.0 (1) | 115.33 (8) | 119.0 (2) | 117.1 (2) |
O21-P2-O22 | 110.79 (15) | 114.0 (1) | 102.8 (1) | 106.4 (1) | 110.9 (2) | 117.3 (1) | 108.42 (8) | 105.3 (2) | 111.1 (2) |
O20-P2-O22 | 108.90 (15) | 112.3 (1) | 116.1 (1) | 113.9 (1) | 115.7 (2) | 109.0 (1) | 112.28 (8) | 111.2 (2) | 105.7 (2) |
C2-N3-C4 | 124.1 (3) | | | | | | | | |
| | | | | | | | | |
C15-C14-N9-C10 | -77.6 (4) | -104.6 (3) | -79.0 (3) | 78.2 (3) | 104.1 (8) | -78.6 (4) | 75.9 (2) | -104.8 (5) | 77.4 (5) |
N9-C14-C15-P1 | -56.7 (3) | 58.3 (2) | -59.5 (3) | 62.8 (3) | -59.4 (7) | -162.3 (2) | 63.8 | 167.9 (3) | -167.7 (3) |
N9-C14-C15-P2 | -179.3 (2) | -177.7 (2) | 175.3 (2) | -171.5 (2) | 177.1 (5) | 76.6 (3) | -170.5 (1) | 46.4 (4) | 69.0 (4) |
N9-C14-C15-O16 | 62.9 (3) | -61.6 (2) | 58.7 (3) | -51.7 (3) | 62.2 (7) | -39.8 (3) | -55.3 (2) | -75.5 (5) | -51.5 (4) |
* P-OH distance.
$ O-P-OH angle
(I) - Present structure
1 - Zoledronic acid trihydrate (Ruscica et al., 2010)
2 - Zoledronic acid monohydrate (Sanders et al., 2003)
3 - Hexacoordinated zinc(II) zoledronate (Freire & Vega,
2009a)
4 - Pentacoordinated zinc(II) zoledronate (Freire & Vega,
2009b)
5 - Potassium complex of zoledronate (Freire et al.,
2010a)
6 - Sodium complex of zoledronate (Freire et al.,
2010b) |
The interaction of drugs with DNA is among the most important aspects of biological studies in drug discovery and pharmaceutical development processes. A number of clinically important small molecules appear to act by binding directly to DNA, and subsequently inhibiting gene expression or replication by interfering with the enzymes that catalyse these functions (Krugh, 1994). Hydrogen bonding plays a pivotal role in biomolecular structure and functions. In the case of nucleosides, the building blocks of DNA and RNA, hydrogen bonding is one of the most important structural features governing their biological role. Cytosine is well known for its hydrogen-bonding capabilities in DNA and RNA, and several cytosine derivatives have been reported for use in biological applications (Blackburn & Gait, 1996; Kumar & Leonard, 1988).
Zoledronic acid or zoledronate (marketed by Novartis under the trade names Zometa, Zomera, Aclasta and Reclast), a potent bone antiresorptive bisphosphonate drug, is used to prevent skeletal fractures in patients with cancers such as multiple myeloma and prostate cancer. It can also be used to treat osteoporosis, hypercalcaemia of malignancy and pain from bone metastases (Reid, 2002; Black et al., 2007), and to prevent recurring fractures in patients with a previous hip fracture (Lyles et al., 2007). Compared with other bisphosphonate drugs, zoledronic acid has superior potency and pharmacological properties. To the best of our knowledge, we report here for the first time a nucleobase–drug interaction, namely the title compound, cytosinium zoledronate trihydrate, (I), in continuation of our ongoing studies of hydrogen-bond interactions and molecular recognition of nucleobases in the solid state (Sridhar & Ravikumar, 2007, 2008, 2010a,b; Sridhar et al., 2009).
The asymmetric unit of (I) contains one cytosinium cation, one zoledronate anion and three water molecules (Fig. 1). Cytosine is quite a strong base (pKα1 = 1.6 and pKα2 = 12.2; Stecher, 1968) and, in the presence of acids, it is readily protonated at the N3 ring position. The cytosinium cation in (I) is protonated at N3, leading to an increase in the internal angle, C2—N3—C4 = 124.1 (3)°, compared with the neutral cytosine molecule [C—N—C = 119.4 (2)°; McClure & Craven, 1973]. Proton transfer is taking place from one of the phosphonic acid groups of the zoledronate molecule to atom N3 of the cytosine molecule.
Zoledronic acid is a bisphosphonic acid, a heterocyclic nitrogen-containing bisphosphonate that has an imidazole-ring side chain. The imidazole ring contains two critically positioned N atoms. The zoledronate group presents its usual zwitterionic character (Vega et al., 1996, 1998), with negative charges in the singly protonated phosphonate groups and a positive charge at protonated imidazole atom N11. The resulting single negative charge is counter-balanced by the protonation of atom N3 of the cytosine molecule. The bond distances and angles are within normal ranges (Allen et al., 1987) and are comparable with the corresponding values observed in zoledronic acid monohydrate (Sanders et al., 2003), zoledronic acid trihydrate (Ruscica et al., 2010), hexa- and pentacoordinated zinc(II)–zoledronate complexes (Freire & Vega, 2009a,b), and potassium and sodium complexes of zoledronate (Freire et al., 2010a,b).
It has already been reported that the P—O bonds in which the O atom is unprotonated are between 1.47 and 1.53 Å long, while in the case of a protonated O atom it increases to 1.54–1.60 Å (Gossman et al., 2003). The P—O distances of (I), as seen in Table 1, are in good agreement with the fact that a protonated P—O bond is slightly longer than an unprotonated P—O bond. The electronic state of the PO3 group can be seen from the O—P—O bond angles. The O—P—O(H) angles are in the range 108.9–110.8°, while the O—P—O angles are in the range 115.7–116.8° (Table 1). Similar behaviour was observed in previously reported zoledronate structures (Sanders et al., 2003; Ruscica et al., 2010; Freire et al., 2010a,b).
An overlay of the zoledronate molecules (Fig. 2), superimposing the planar imidazole ring, reveals the significant orientational differences between the phosphonate groups. The relative orientations of the imidazole rings can be seen from the C15—C14—N9—C10 torsion angles (Table 1). In (I), it adopts a synclinal orientation, while the previously reported zoledronate structures have either synclinal (±30–90°) or anticlinal (±90–150°) orientations (Table 1). Of these nine reported structures [including (I), Table 1], six molecules exist in a synclinal orientation and the remaining three are in an anticlinal orientation. The orientation of the phosphonate (P1 and P2) groups of the zoledronate anion can be seen from the N9—C14—C15—P1 and N9—C14—C15—P2 torsion angles. It can be seen that the phosphonate groups prefer to adopt either a synclinal (±30–90°) or an antiperiplanar (±150–180°) orientation. In (I), atom P1 is in a synclinal orientation and P2 is in an antiperiplanar orientation. In the case of the hydroxyl group (torsion angle N9—C14—C15—O16), all the structures adopt a synclinal (±30–90°) orientation (Table 1). The above change observed in the conformation of the solid-state structures of zoledronate may be attributed to the different environments of the zoledronic acid: hydrates or metal-coordinated.
In the crystal packing of (I), the component ions are linked into complex three-dimensional networks by a combination of X—H···O (X = N and O) hydrogen bonds (Table 2). A detailed analysis of the hydrogen-bonding scheme reveals that there are 16 potential active H atoms (four from each cation and anion, and eight from water). Five different modes of hydrogen-bonding interaction are observed, viz. cation–cation, anion–anion, cation–anion, cation–water and anion–water.
The cytosinium cations are linked through an N—H···O hydrogen bond, forming a C6 chain (Etter, 1990; Etter et al., 1990; Bernstein et al., 1995) parallel to the b axis. The zoledronate anions form a centrosymmetric dimer [R22(16)] through an N—H···O hydrogen bond. The O—H···O hydrogen bonds between symmetry-related dimers of the phosphonate groups of the zoledronate anion form a ribbon parallel to the b axis. These hydrogen bonds form a rather rectangular-shaped centrosymmetric tetramer and produce a characteristic R44(26) motif (Fig. 3).
The cytosinium cation and zoledronate anion are held together by two N—H···O hydrogen bonds (entries 2 and 3, Table 2), thereby generating an R22(10) motif. Intermolecular N—H···O and O—H···O interactions link adjacent R22(10) motifs to produce another R43(12) motif. Thus, the combination of N—H···O and O—H···O bonds leads to the formation of a one-dimensional polymeric ribbon along the b axis, in which the zoledronate anions are flanked by the cytosinium cations (Fig. 3).
The water molecules (O1W, O2W and O3W) play a dual role as both donors and acceptors in the hydrogen-bonding interactions (Table 2). The two water molecules O1W and O2W, as donors and acceptors, link three zoledronate anions through O—H···O hydrogen bonds, while the third water molecule (O3W) links two zoledronate anions as donor, and acts as acceptor in linking the cytosinium cation via an N—H···O hydrogen bond.
Water molecule O1W, acting as donor, links the two symmetry-related atoms O18(x, y + 1, z) and O20(x, y + 1, z) of the zoledronate anion through three-centred hydrogen bonds (Jeffrey & Saenger, 1991) to form an R12(6) motif. As acceptor, it links atom O19(x + 1,y - 1,z) of the anion and forms an infinite anion–water chain along the a axis. The second water molecule, O2W, as donor and acceptor, links the anion–water chain via atoms O21 and O16(x + 1,y,z) to form a tetrameric hydrogen-bonded network of R44(15) motif. Furthermore, the two water molecules O1W and O2W link the R44(15) tetramers through O—H···O hydrogen bonds involving atoms O21 and O17(x - 1,y + 1,z) of the anions and form another set of tetrameric hydrogen-bonded networks of R43(10) motif. The R44(15) and R43(10) motifs are arranged alternately and aggregate as infinite two-dimensional hydrogen-bonded layers parallel to the (001) plane (Fig.4).
As donor, the third water molecule, O3W, forms hydrogen bonds to atoms O19(-x + 2, -y + 1, -z + 1), O22(-x + 2, -y + 1, -z + 1) and atom O20(-x + 1, -y + 1, -z + 1) of the zoledronate anion, forming an R12(6) motif (three-centred hydrogen bonds), resulting in an infinite anion–water chain along the a axis. In addition, atom O3W acts as acceptor in a hydrogen bond from atom N1 of the cytosinium cation. Thus, the water molecule bridges the cation and anion through N—H···O and O—H···O hydrogen bonds and leads to the formation of a one-dimensional chain with alternate cations and anions (Fig. 5).
Thus, the combination of N—H···O and O—H···O hydrogen bonds involving cations, anions and water molecules leads to the formation of three-dimensional hydrogen-bonded networks (Fig. 6). This structure displays segregation of its molecular components.
C—H···O interactions are also observed in the crystal structure of (I). Incidentally, the C—H···O interaction between the imidazole and biphosphonate group [C13—H13···O21(x, -1 + y, z)] is one of the most favourable interactions observed in zoledronate complexes (Freire et al., 2010a,b). It is very interesting to note that there is no water–water interaction in the structure of (I).