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In the asymmetric unit of the title compound, C5H7N5O2+·2NO3-·2H2O, the guanine base is diprotonated and cocrystallizes with two nitrate anions and two water molecules. The structure is a layered one, and in each layer all H atoms bonded to O and N atoms are involved in a two-dimensional hydrogen-bonding network. Short contacts are observed between parallel layers and ensure the cohesion of the crystals.
Supporting information
CCDC reference: 202339
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.002 Å
- R factor = 0.045
- wR factor = 0.124
- Data-to-parameter ratio = 10.5
checkCIF results
No syntax errors found
ADDSYM reports no extra symmetry
Alert Level C:
PLAT_353 Alert C Long N-H Bond (0.87A) N(7) - H(7) = 1.02 Ang.
PLAT_353 Alert C Long N-H Bond (0.87A) N(9) - H(9) = 1.01 Ang.
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
2 Alert Level C = Please check
Guaninium dinitrate dihydrate was prepared from a solution of 1 mmol guanine and 2 mmol nitric acid in 10 ml water. Colorless crystals were formed upon slow evaporation of the solution over a period of two weeks.
All H atoms were refined isotropically at localized positions.
Data collection: KappaCCD Reference Manual (Nonius, 1998); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997) and CAMERON (Watkin et al., 1993); software used to prepare material for publication: WinGX (Farrugia, 1999).
Crystal data top
C5H7N5O2+·2NO3−·2H2O | F(000) = 648 |
Mr = 313.21 | Dx = 1.657 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 8447 reflections |
a = 6.6340 (4) Å | θ = 3.1–26.4° |
b = 11.9800 (5) Å | µ = 0.16 mm−1 |
c = 15.8040 (3) Å | T = 293 K |
β = 91.01 (2)° | Prism, colorless |
V = 1255.83 (10) Å3 | 0.60 × 0.45 × 0.40 mm |
Z = 4 | |
Data collection top
Nonius KappaCCD diffractometer | 2103 reflections with I > 2σ(I)) |
Radiation source: fine-focus sealed tube | Rint = 0.049 |
Graphite monochromator | θmax = 26.4°, θmin = 3.1° |
ϕ scans | h = −7→8 |
8447 measured reflections | k = −14→14 |
2447 independent reflections | l = −19→19 |
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)] = 0.045 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.124 | All H-atom parameters refined |
S = 1.07 | w = 1/[σ2(Fo2) + (0.049P)2 + 0.3341P] where P = (Fo2 + 2Fc2)/3 |
2447 reflections | (Δ/σ)max = 0.020 |
234 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
Crystal data top
C5H7N5O2+·2NO3−·2H2O | V = 1255.83 (10) Å3 |
Mr = 313.21 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 6.6340 (4) Å | µ = 0.16 mm−1 |
b = 11.9800 (5) Å | T = 293 K |
c = 15.8040 (3) Å | 0.60 × 0.45 × 0.40 mm |
β = 91.01 (2)° | |
Data collection top
Nonius KappaCCD diffractometer | 2103 reflections with I > 2σ(I)) |
8447 measured reflections | Rint = 0.049 |
2447 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.045 | 0 restraints |
wR(F2) = 0.124 | All H-atom parameters refined |
S = 1.07 | Δρmax = 0.19 e Å−3 |
2447 reflections | Δρmin = −0.22 e Å−3 |
234 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. |
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 | |
O12 | 0.1344 (3) | 0.53124 (11) | 0.39602 (9) | 0.0631 (4) | |
O11 | 0.0230 (3) | 0.61145 (14) | 0.28256 (10) | 0.0734 (5) | |
O13 | 0.0589 (3) | 0.43204 (13) | 0.28621 (9) | 0.0674 (4) | |
N11 | 0.0710 (2) | 0.52604 (13) | 0.32016 (9) | 0.0485 (4) | |
O2W | −0.1403 (3) | 0.43654 (12) | 0.13177 (11) | 0.0760 (6) | |
O1W | 0.2164 (2) | 0.75207 (13) | 0.45477 (10) | 0.0599 (4) | |
N9 | 0.1856 (2) | 0.31258 (12) | 0.44269 (8) | 0.0401 (3) | |
N21 | 0.3793 (2) | 0.61465 (12) | 0.63401 (8) | 0.0415 (3) | |
C4 | 0.2657 (2) | 0.27262 (12) | 0.51618 (10) | 0.0356 (3) | |
N3 | 0.3334 (2) | 0.33209 (12) | 0.58462 (8) | 0.0384 (3) | |
N7 | 0.1877 (2) | 0.13073 (12) | 0.43414 (9) | 0.0448 (3) | |
C6 | 0.3424 (2) | 0.09195 (14) | 0.58112 (11) | 0.0425 (4) | |
N1 | 0.4020 (2) | 0.16197 (12) | 0.64958 (9) | 0.0431 (4) | |
O23 | 0.3629 (2) | 0.71799 (10) | 0.63284 (9) | 0.0578 (4) | |
C8 | 0.1391 (3) | 0.22351 (14) | 0.39439 (11) | 0.0451 (4) | |
O6 | 0.3555 (2) | −0.00821 (11) | 0.58649 (9) | 0.0603 (4) | |
O21 | 0.4429 (2) | 0.56608 (11) | 0.69824 (8) | 0.0591 (4) | |
N2 | 0.4731 (3) | 0.32712 (15) | 0.71854 (10) | 0.0509 (4) | |
C2 | 0.4041 (2) | 0.27413 (13) | 0.65179 (10) | 0.0387 (4) | |
C5 | 0.2695 (2) | 0.15926 (13) | 0.51179 (10) | 0.0395 (4) | |
O22 | 0.3339 (3) | 0.55972 (11) | 0.57020 (9) | 0.0737 (5) | |
H23 | −0.156 (4) | 0.376 (3) | 0.1051 (18) | 0.083 (8)* | |
H24 | −0.077 (4) | 0.432 (2) | 0.179 (2) | 0.078 (8)* | |
H12 | 0.180 (4) | 0.683 (3) | 0.436 (2) | 0.089 (9)* | |
H11 | 0.259 (4) | 0.761 (2) | 0.507 (2) | 0.082 (8)* | |
H8 | 0.080 (3) | 0.2267 (17) | 0.3423 (14) | 0.049 (5)* | |
H1 | 0.451 (4) | 0.128 (2) | 0.6937 (17) | 0.067 (6)* | |
H7 | 0.167 (4) | 0.053 (2) | 0.4097 (17) | 0.073 (7)* | |
H21 | 0.473 (3) | 0.403 (2) | 0.7170 (14) | 0.059 (6)* | |
H9 | 0.164 (4) | 0.393 (2) | 0.4254 (16) | 0.078 (7)* | |
H22 | 0.530 (4) | 0.292 (2) | 0.7619 (16) | 0.065 (7)* | |
H3 | 0.338 (3) | 0.407 (2) | 0.5823 (14) | 0.061 (6)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O12 | 0.0969 (11) | 0.0459 (7) | 0.0455 (7) | 0.0012 (7) | −0.0228 (7) | 0.0042 (6) |
O11 | 0.0946 (12) | 0.0618 (9) | 0.0634 (9) | 0.0129 (8) | −0.0140 (8) | 0.0242 (7) |
O13 | 0.0939 (11) | 0.0568 (9) | 0.0507 (8) | 0.0069 (7) | −0.0251 (7) | −0.0022 (6) |
N11 | 0.0498 (8) | 0.0523 (9) | 0.0432 (8) | 0.0030 (7) | −0.0065 (6) | 0.0107 (7) |
O2W | 0.1257 (15) | 0.0380 (8) | 0.0627 (9) | −0.0062 (8) | −0.0455 (10) | 0.0022 (6) |
O1W | 0.0749 (10) | 0.0481 (8) | 0.0566 (9) | 0.0034 (7) | −0.0043 (7) | 0.0105 (7) |
N9 | 0.0475 (7) | 0.0358 (7) | 0.0368 (7) | 0.0041 (6) | −0.0044 (5) | 0.0042 (5) |
N21 | 0.0508 (8) | 0.0358 (7) | 0.0376 (7) | −0.0026 (5) | −0.0064 (6) | −0.0039 (5) |
C4 | 0.0369 (7) | 0.0328 (8) | 0.0372 (8) | 0.0035 (6) | 0.0011 (6) | 0.0044 (6) |
N3 | 0.0473 (7) | 0.0309 (7) | 0.0368 (7) | 0.0047 (5) | −0.0034 (5) | 0.0060 (5) |
N7 | 0.0528 (8) | 0.0365 (7) | 0.0448 (7) | 0.0024 (6) | −0.0055 (6) | −0.0018 (6) |
C6 | 0.0460 (8) | 0.0327 (8) | 0.0487 (9) | 0.0052 (6) | 0.0015 (7) | 0.0078 (7) |
N1 | 0.0500 (8) | 0.0366 (7) | 0.0425 (8) | 0.0048 (6) | −0.0034 (6) | 0.0128 (6) |
O23 | 0.0868 (10) | 0.0328 (6) | 0.0533 (8) | −0.0001 (6) | −0.0162 (7) | −0.0048 (5) |
C8 | 0.0513 (9) | 0.0442 (9) | 0.0396 (9) | 0.0041 (7) | −0.0054 (7) | 0.0004 (7) |
O6 | 0.0814 (9) | 0.0313 (6) | 0.0681 (9) | 0.0065 (6) | −0.0069 (7) | 0.0095 (6) |
O21 | 0.0911 (10) | 0.0428 (7) | 0.0425 (7) | 0.0022 (6) | −0.0237 (6) | −0.0030 (5) |
N2 | 0.0652 (10) | 0.0437 (9) | 0.0432 (8) | 0.0046 (7) | −0.0114 (7) | 0.0043 (6) |
C2 | 0.0411 (8) | 0.0379 (8) | 0.0371 (8) | 0.0048 (6) | 0.0005 (6) | 0.0071 (6) |
C5 | 0.0429 (8) | 0.0339 (8) | 0.0417 (8) | 0.0030 (6) | −0.0005 (6) | 0.0026 (6) |
O22 | 0.1369 (15) | 0.0387 (7) | 0.0443 (7) | −0.0020 (8) | −0.0343 (8) | −0.0065 (5) |
Geometric parameters (Å, º) top
O12—N11 | 1.265 (2) | N3—C2 | 1.3459 (19) |
O11—N11 | 1.223 (2) | N3—H3 | 0.90 (3) |
O13—N11 | 1.249 (2) | N7—C8 | 1.314 (2) |
O2W—H23 | 0.84 (3) | N7—C5 | 1.376 (2) |
O2W—H24 | 0.86 (3) | N7—H7 | 1.02 (3) |
O1W—H12 | 0.91 (3) | C6—O6 | 1.206 (2) |
O1W—H11 | 0.87 (3) | C6—N1 | 1.420 (2) |
N9—C8 | 1.345 (2) | C6—C5 | 1.437 (2) |
N9—C4 | 1.356 (2) | N1—C2 | 1.344 (2) |
N9—H9 | 1.01 (3) | N1—H1 | 0.87 (3) |
N21—O22 | 1.2369 (18) | C8—H8 | 0.90 (2) |
N21—O21 | 1.2376 (18) | N2—C2 | 1.307 (2) |
N21—O23 | 1.2429 (18) | N2—H21 | 0.91 (3) |
C4—C5 | 1.360 (2) | N2—H22 | 0.88 (3) |
C4—N3 | 1.365 (2) | | |
| | | |
O11—N11—O13 | 122.10 (16) | C5—N7—H7 | 127.9 (15) |
O11—N11—O12 | 119.92 (17) | O6—C6—N1 | 121.03 (15) |
O13—N11—O12 | 117.98 (14) | O6—C6—C5 | 129.40 (17) |
H23—O2W—H24 | 116 (3) | N1—C6—C5 | 109.57 (14) |
H12—O1W—H11 | 120 (3) | C2—N1—C6 | 127.80 (14) |
C8—N9—C4 | 106.77 (13) | C2—N1—H1 | 116.6 (17) |
C8—N9—H9 | 124.9 (15) | C6—N1—H1 | 115.4 (17) |
C4—N9—H9 | 128.3 (15) | N7—C8—N9 | 110.35 (15) |
O22—N21—O21 | 119.55 (14) | N7—C8—H8 | 124.7 (13) |
O22—N21—O23 | 119.85 (14) | N9—C8—H8 | 125.0 (13) |
O21—N21—O23 | 120.60 (13) | C2—N2—H21 | 117.7 (14) |
N9—C4—C5 | 108.43 (14) | C2—N2—H22 | 122.1 (15) |
N9—C4—N3 | 127.81 (13) | H21—N2—H22 | 120 (2) |
C5—C4—N3 | 123.76 (14) | N2—C2—N1 | 120.64 (15) |
C2—N3—C4 | 117.45 (14) | N2—C2—N3 | 119.88 (15) |
C2—N3—H3 | 122.4 (15) | N1—C2—N3 | 119.47 (15) |
C4—N3—H3 | 119.9 (15) | C4—C5—N7 | 106.63 (14) |
C8—N7—C5 | 107.81 (14) | C4—C5—C6 | 121.84 (15) |
C8—N7—H7 | 124.3 (15) | N7—C5—C6 | 131.49 (15) |
| | | |
C8—N9—C4—C5 | 0.66 (18) | C4—N3—C2—N1 | −1.2 (2) |
C8—N9—C4—N3 | −179.39 (16) | N9—C4—C5—N7 | −0.63 (18) |
N9—C4—N3—C2 | 178.79 (15) | N3—C4—C5—N7 | 179.41 (14) |
C5—C4—N3—C2 | −1.3 (2) | N9—C4—C5—C6 | −178.57 (14) |
O6—C6—N1—C2 | 177.04 (16) | N3—C4—C5—C6 | 1.5 (2) |
C5—C6—N1—C2 | −3.3 (2) | C8—N7—C5—C4 | 0.36 (19) |
C5—N7—C8—N9 | 0.05 (19) | C8—N7—C5—C6 | 178.03 (17) |
C4—N9—C8—N7 | −0.44 (19) | O6—C6—C5—C4 | −179.75 (18) |
C6—N1—C2—N2 | −176.53 (16) | N1—C6—C5—C4 | 0.7 (2) |
C6—N1—C2—N3 | 3.8 (3) | O6—C6—C5—N7 | 2.9 (3) |
C4—N3—C2—N2 | 179.11 (15) | N1—C6—C5—N7 | −176.71 (16) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N(1)—H(1)···O(21)i | 0.87 (3) | 1.98 (3) | 2.8417 (19) | 174 (2) |
N(3)—H(3)···O(22) | 0.90 (2) | 1.84 (2) | 2.737 (2) | 176 (2) |
N(7)—H(7)···O(2W)ii | 1.02 (2) | 1.55 (2) | 2.566 (2) | 177 (2) |
N(9)—H(9)···O(12) | 1.01 (2) | 1.73 (2) | 2.741 (2) | 178 (1) |
N(9)—H(9)···O(13) | 1.01 (2) | 2.34 (3) | 2.966 (2) | 119 (2) |
O(1W)—H(11)···O(23) | 0.87 (3) | 2.16 (3) | 2.989 (2) | 159 (2) |
O(1W)—H(12)···O(12) | 0.91 (4) | 1.95 (4) | 2.853 (2) | 174 (2) |
N(2)—H(21)···O(21) | 0.91 (2) | 1.99 (2) | 2.887 (2) | 171 (2) |
N(2)—H(22)···O(23)i | 0.88 (3) | 2.00 (3) | 2.884 (2) | 174 (3) |
O(2W)—H(23)···O(1W)ii | 0.84 (3) | 1.80 (3) | 2.643 (2) | 174 (3) |
O(2W)—H(24)···O(13) | 0.85 (3) | 1.91 (3) | 2.756 (2) | 176 (2) |
C(8)—H(8)···O(11)ii | 0.91 (2) | 2.49 (2) | 3.267 (2) | 144 (2) |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x, y−1/2, −z+1/2. |
Experimental details
Crystal data |
Chemical formula | C5H7N5O2+·2NO3−·2H2O |
Mr | 313.21 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 293 |
a, b, c (Å) | 6.6340 (4), 11.9800 (5), 15.8040 (3) |
β (°) | 91.01 (2) |
V (Å3) | 1255.83 (10) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.16 |
Crystal size (mm) | 0.60 × 0.45 × 0.40 |
|
Data collection |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I))] reflections | 8447, 2447, 2103 |
Rint | 0.049 |
(sin θ/λ)max (Å−1) | 0.625 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.045, 0.124, 1.07 |
No. of reflections | 2447 |
No. of parameters | 234 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.19, −0.22 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N(1)—H(1)···O(21)i | 0.87 (3) | 1.98 (3) | 2.8417 (19) | 174 (2) |
N(3)—H(3)···O(22) | 0.90 (2) | 1.84 (2) | 2.737 (2) | 176 (2) |
N(7)—H(7)···O(2W)ii | 1.02 (2) | 1.55 (2) | 2.566 (2) | 177 (2) |
N(9)—H(9)···O(12) | 1.01 (2) | 1.73 (2) | 2.741 (2) | 178.4 (14) |
N(9)—H(9)···O(13) | 1.01 (2) | 2.34 (3) | 2.966 (2) | 118.8 (18) |
O(1W)—H(11)···O(23) | 0.87 (3) | 2.16 (3) | 2.989 (2) | 159 (2) |
O(1W)—H(12)···O(12) | 0.91 (4) | 1.95 (4) | 2.853 (2) | 174 (2) |
N(2)—H(21)···O(21) | 0.91 (2) | 1.99 (2) | 2.887 (2) | 171 (2) |
N(2)—H(22)···O(23)i | 0.88 (3) | 2.00 (3) | 2.884 (2) | 174 (3) |
O(2W)—H(23)···O(1W)ii | 0.84 (3) | 1.80 (3) | 2.643 (2) | 174 (3) |
O(2W)—H(24)···O(13) | 0.85 (3) | 1.91 (3) | 2.756 (2) | 176 (2) |
C(8)—H(8)···O(11)ii | 0.91 (2) | 2.49 (2) | 3.267 (2) | 143.5 (17) |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x, y−1/2, −z+1/2. |
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Guanine is a purine base, is a constituent of nucleotides and as such pairs with cytosine in the helical structure of DNA. A number of purine and pyrimidine analogs are effective metabolic inhibitors with useful chemotherapeutic activity (Roy-Burman, 1970; Balis, 1968; Hitchings et al., 1963). This kind of hydrogen bonding in hybrid compounds appears in several binding sites in biological mechanisms of action, for example N—H···O hydrogen bonds between guanine rings and phosphate ions are involved in the active-site inhibitor-binding mechanism in the ternary complex of calf spleen purine nucleoside phosphorylase, it also provides a new starting point for the design of inhibitors of PNP for therapeutic and other applications (Luic et al., 2001). The crystal structures of guanine picrate monohydrate and thioguanine picrate monohydrate (Bugg et al., 1975), and guaninium dichloride (Matkovic-Calogovic et al., 1999) have been reported previously. This work is part of a series of structural studies on hybrid compounds based on organic matrix and inorganic acids; other examples are m-carboxyphenylammonium nitrate (Benali-Cherif & Cherouana et al., 2002), p-carboxyphenylammonium dihydrogenmonophosphate monohydrate (Benali-Cherif, Abouimrane et al., 2002) and L-histidinium dinitrate (Benali-Cherif, Benguedouar et al., 2002). The main purpose of the present study is to look at the hydrogen bonding engineered in the crystals of guanine and nitric acid, the imino groups of the pyrimidine and imidazolyl portions (atoms N3 and N7, respectively) in guanine are protonated, each resulting C5H7N5O2+ dication is surrounded by three nitrate anions and a water molecule (Fig. 1). Protonated N atoms are involved in the strongest hydrogen bonds, indeed atoms N3 and N7 are hydrogen bonded through intermolecular interactions to nitrate [N3—H3···O22 = 2.737 (2) Å] and water O atoms [N7—H7···O2w = 2.566 (2) Å]. The guanine base is doubly linked to a single nitrate anion via intramolecular hydrogen bonds [N1—H1···O21 = 2.8417 (19) Å and N2—H22···O23 = 2.884 (2) Å], while N9 atom of the imidazolyl portion is hydrogen bonded to a nitrate anion by an intermolecular interaction [N9—H9···O12 = 2.741 (2) Å], we also observe close contacts between atoms C8 and O11 [C8—H8···O11 = 3.267 (2) Å]. Atom O1w of water molecule plays an important role in the three-dimensional network of hydrogen bonding. In a layer, atom O1w is bound to two nitrate anions [O1w—H12···O12 = 2.853 (2) Å and O1w—H11···O23 = 2.989 (2) Å] on one hand, and on the other hand to the second molecule of water [O2w—H23···O1w = 2.643 (2) Å]. In each layer, anions, cations and water molecules constitute a two-dimensional network of hydrogen bonding (Fig. 2). The crystal packing (Fig. 3) is constituted by arrangement of parallel layers along the b axis. This packing is stabilized by short contacts, the strongest being observed between atoms C2 and O1w [C2···O1w = 3.070(?)Å]. The torsion angles around atoms C4 and C5 [N9—C4—N3—C2 = 178.79 (15)° and N1—C6—C5—N7 = −176.71 (16)°] show clearly that the purine base geometry is not affected by protonation of atoms N3 and N7, thus the imidazolyl and pyrimidine rings are coplanar.