Guaninium dinitrate dihydrate

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.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](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

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S1. Comment

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.

S2. Experimental

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.

S3. Refinement

All H atoms were refined isotropically at localized positions.

Computing details

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).

Figures

	Fig. 1. An ORTEP-3 (Farrugia, 1997) view with the atomic labelling scheme, showing the asymmetric unit of (I). Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Packing diagram of the title compound, viewed down the a axis, showing a two-dimensional network of hydrogen bonds.
	Fig. 3. An ORTEP-3 (Farrugia, 1997) diagram of the layered packing in (I), viewed down the b axis.

(I)

Crystal data

C5H7N5O^2+·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) Å^3	0.60 × 0.45 × 0.40 mm
Z = 4

Data collection

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

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.045	Hydrogen site location: difference Fourier map
wR(F^2) = 0.124	All H-atom parameters refined
S = 1.07	w = 1/[σ^2(Fo^2) + (0.049P)^2 + 0.3341P] where P = (Fo^2 + 2Fc^2)/3
2447 reflections	(Δ/σ)max = 0.020
234 parameters	Δρmax = 0.19 e Å^−3
0 restraints	Δρmin = −0.22 e Å^−3

Special details

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 (Ų)

	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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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)

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.