Diprotonated adeninium diperchlorate hydrate at 120 K

In the title compound, C₅H₉N₅²⁺·2ClO₄⁻·H₂O, the structure can be described as alternating layers of C₅H₉N₅²⁺ and ClO₄⁻ ions along the a axis. Layers of adeninium cations and perchlorate anions are linked by strong anion–cation and anion–water hydrogen bonds via the sandwiched water mol­ecules. This three-dimensional complex network of hydrogen bonds (N—H...O) reinforces the cohesion of the ionic structure.

Key indicators

• Single-crystal X-ray study
• T = 120 K
• Mean [sigma](C-C) = 0.002 Å
• Disorder in solvent or counterion
• R factor = 0.036
• wR factor = 0.105
• Data-to-parameter ratio = 22.4

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



PLAT_302  Alert C Anion/Solvent Disorder .......................       8.00 Perc.


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

---

S1. Comment

Structure elucidation of components of nucleic acids and their derivatives are of interest, because of their widespread biological occurrence (Richards et al., 1972; Perutz & Ten Eyck, 1972). Adenine is one of the precursors of DNA and RNA nucleotides, along with cytosine, guanine, thymine, and uracil. The cystal structures of adenine hydrochloride hemihydrate (Cunane & Taylor, 1997), adenine hydrobromide hemihydrate (Langer & Huml, 1978a), adenine dihydrochloride (Kistenmacher & Shigematsu, 1974), adeninium dinitrate (Hardgrove et al., 1983), adeninium phosphate (Langer et al., 1979), adeninium sulfate (Langer & Huml, 1978b), and adeninium hemisulfate hydrate (Langer et al., 1978) have been reported. In several crystal structures of compounds with organic bases, amino acides and inorganic acids, the structural cohesion is assured by strong hydrogen bonds, as was observed in m-carboxyphenylammonium nitrate (Benali-Cherif, Cherouana et al., 2002) and L-histidinium dinitrate (Benali-Cherif, Benguedouar et al., 2002), phosphoric: m-carboxyphenylammonium phosphate (Benali-Cherif, Bendheif et al., 2002) and p-carboxyphenylammonium dihydrogenmonophosphate monohydrate (Benali-Cherif, Abouimrane et al., 2002), guaninium dinitrate dihydrate (Bouchouit et al., 2002), guaninium sulfate monohydrate (Cherouana et al., 2003) and L-valinium monohydrogenphosphite (Bendheif et al., 2003). The main purpose of the present study is to examine the hydrogen bonding engineered in the crystals of diprotonated adeninium diperchlorate hydrate, (I), at 120 K.

The strucure determination reveals that imidazolyl and pyrimidine rings are coplanar. The perchlorate ions are slightly disordered at 120 K, but remains tetrahedral in shape with Cl—O distances and O—Cl—O angles ranging from 1.4413 (11) to 1.471 (5) Å and 107.9 (3) to 121.6 (2)°. Two imino groups of imidazolyl and pyrimidine moieties of adenine base are protonated at positions N1 and N7 as already reported in various crystal structures containing adenine cations (adeninium sulfate, adenine dihydrochloride and adeninium dinitrate). This is evident from the increase in the ring angle at the site of protonation, namely N1 and N7. The internal angles at N1 and N7 [C6—N1—C2 = 124.02 (15)° and C8—N7—C5 = 108.31 (14)°] have increased from the reported 119.8° and 104.4° values in the unprotonated adenine (Voet & Rich, 1970). The diprotonated adenenium cation and perchlorate anion are linked by hydrogen bonds (Table 2 and Fig. 2). N1, N6, N7 and N9 atoms are involved in the strongest intramolecular and intermolecular N—H···O hydrogen bonds with perchlorate anions. We also observed that the water molecule forms five hydrogen bonds with the adeninium and perchlorate ions, in two modes, as donnor with perchlorate anion and adeninium ion respectively and as acceptor with the adeninium ion (Table 2).

S2. Experimental

The title compound was obtained as colorless crystals, after few days, by slow evaporation from an aqueous solution of adenine and perchloric acid in stoichiometric ratio of 1:2.

S3. Refinement

In the initial refinement of the title compound, atom O5 of one perchlorate anion showed large anisotropy of apparent thermal motion. The final refinement was carried out with a model in which O5 is distributed on two sites with equal occupancy (O5A and O5B) to simulate a disorder that occurs by a twist around the Cl2—O5 arm.

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: SIR2002 (Burla et al., 2003); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrujia, 1997) and PLUTON (Spek, 1990); software used to prepare material for publication: WinGX (Farrugia, 1999) and PARST (Nardelli, 1995).

Figures

	Fig. 1. An ORTEP-3 (Farrugia, 1997) view of title compound with the atom-numbering scheme and 50% probability displacement ellipsoids.
	Fig. 2. PLUTON (Spek, 1990) view of the ionic structure, showing the imediate hydrogen-bonded surroundings of anions and cation.

(I)

Crystal data

C5H7N5^2+·2ClO4^2^−·H2O	Z = 2
Mr = 354.07	F(000) = 360
Triclinic, P1	Dx = 1.903 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 7.7777 (2) Å	Cell parameters from 14891 reflections
b = 8.5114 (2) Å	θ = 2.0–33.1°
c = 11.0871 (3) Å	µ = 0.59 mm^−1
α = 88.703 (2)°	T = 120 K
β = 70.074 (2)°	Needle, colorless
γ = 64.789 (2)°	0.3 × 0.2 × 0.1 mm
V = 617.78 (3) Å^3

Data collection

Nonius KappaCCD diffractometer	3520 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.030
Graphite monochromator	θmax = 33.1°, θmin = 2.0°
ϕ scans	h = −10→11
14891 measured reflections	k = −11→13
4647 independent reflections	l = −16→16

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)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.105	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ^2(Fo^2) + (0.058P)^2] where P = (Fo^2 + 2Fc^2)/3
4647 reflections	(Δ/σ)max = 0.003
207 parameters	Δρmax = 0.48 e Å^−3
4 restraints	Δρmin = −0.60 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Cl1	0.33276 (5)	0.30700 (4)	0.04545 (3)	0.01462 (8)
Cl2	0.09320 (6)	0.73038 (4)	0.47966 (3)	0.02185 (10)
O1	0.39018 (18)	0.40062 (16)	−0.05868 (12)	0.0285 (3)
O3	0.51275 (15)	0.16082 (13)	0.05086 (10)	0.0184 (2)
O6	0.17584 (18)	0.55024 (14)	0.50410 (11)	0.0275 (3)
O4	0.19887 (17)	0.24322 (14)	0.02364 (12)	0.0240 (2)
O8	0.22430 (17)	0.74387 (15)	0.35731 (12)	0.0262 (3)
O2	0.22803 (17)	0.42359 (14)	0.16684 (11)	0.0268 (3)
O1W	0.22631 (17)	0.41867 (14)	0.72967 (11)	0.0186 (2)
N1	0.47554 (17)	0.20666 (15)	0.32794 (11)	0.0148 (2)
H1	0.3492	0.2554	0.3785	0.018*
N7	0.94493 (17)	−0.20159 (14)	0.18786 (11)	0.0126 (2)
H7	0.9362	−0.2985	0.1998	0.015*
O7	−0.10692 (17)	0.77912 (17)	0.47463 (12)	0.0360 (3)
N3	0.75792 (18)	0.25921 (14)	0.20731 (11)	0.0144 (2)
N9	1.07032 (17)	−0.01574 (14)	0.12476 (11)	0.0136 (2)
H9	1.1569	0.0249	0.0891	0.016*
N6	0.47791 (19)	−0.06836 (16)	0.34398 (13)	0.0208 (3)
H6A	0.3488	−0.0194	0.3883	0.025*
H6B	0.5441	−0.1808	0.3266	0.025*
C5	0.7845 (2)	−0.03561 (16)	0.22907 (12)	0.0122 (2)
C8	1.1134 (2)	−0.18642 (17)	0.12718 (13)	0.0143 (3)
H8	1.2432	−0.2797	0.0912	0.017*
C4	0.8640 (2)	0.08223 (17)	0.18914 (12)	0.0120 (2)
C6	0.5737 (2)	0.02835 (17)	0.30290 (13)	0.0139 (2)
C2	0.5652 (2)	0.31327 (18)	0.27776 (14)	0.0161 (3)
H2	0.4823	0.4337	0.2953	0.019*
O5A	0.0368 (9)	0.8396 (9)	0.5939 (6)	0.0414 (13)	0.50
O5B	0.1143 (8)	0.8443 (9)	0.5674 (6)	0.0388 (12)	0.50
H1W	0.188 (3)	0.451 (3)	0.6707 (16)	0.047 (5)*
H2W	0.232 (3)	0.482 (2)	0.7765 (18)	0.047 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.01297 (15)	0.01232 (14)	0.01924 (16)	−0.00603 (12)	−0.00618 (12)	0.00278 (11)
Cl2	0.0274 (2)	0.01333 (15)	0.01695 (17)	−0.00175 (14)	−0.00851 (14)	0.00041 (12)
O1	0.0299 (6)	0.0332 (6)	0.0342 (7)	−0.0219 (6)	−0.0163 (5)	0.0212 (5)
O3	0.0132 (5)	0.0140 (5)	0.0227 (5)	−0.0015 (4)	−0.0062 (4)	0.0000 (4)
O6	0.0281 (6)	0.0142 (5)	0.0262 (6)	−0.0011 (5)	−0.0049 (5)	0.0058 (4)
O4	0.0218 (6)	0.0228 (5)	0.0377 (6)	−0.0153 (5)	−0.0161 (5)	0.0086 (5)
O8	0.0205 (6)	0.0276 (6)	0.0338 (7)	−0.0146 (5)	−0.0092 (5)	0.0129 (5)
O2	0.0211 (6)	0.0190 (5)	0.0283 (6)	0.0017 (5)	−0.0085 (5)	−0.0076 (4)
O1W	0.0207 (5)	0.0140 (5)	0.0222 (5)	−0.0091 (4)	−0.0071 (4)	0.0013 (4)
N1	0.0101 (5)	0.0123 (5)	0.0176 (5)	−0.0035 (4)	−0.0018 (4)	0.0010 (4)
N7	0.0120 (5)	0.0084 (5)	0.0150 (5)	−0.0031 (4)	−0.0041 (4)	0.0014 (4)
O7	0.0138 (5)	0.0369 (7)	0.0374 (7)	−0.0019 (5)	0.0008 (5)	0.0173 (6)
N3	0.0139 (5)	0.0104 (5)	0.0179 (5)	−0.0045 (4)	−0.0058 (4)	0.0019 (4)
N9	0.0108 (5)	0.0130 (5)	0.0163 (5)	−0.0059 (4)	−0.0032 (4)	0.0023 (4)
N6	0.0129 (6)	0.0144 (5)	0.0292 (7)	−0.0063 (5)	−0.0007 (5)	0.0026 (5)
C5	0.0118 (6)	0.0104 (5)	0.0130 (6)	−0.0040 (5)	−0.0040 (5)	0.0011 (4)
C8	0.0132 (6)	0.0124 (6)	0.0155 (6)	−0.0041 (5)	−0.0053 (5)	0.0013 (5)
C4	0.0112 (6)	0.0111 (5)	0.0131 (6)	−0.0045 (5)	−0.0044 (5)	0.0005 (4)
C6	0.0123 (6)	0.0133 (6)	0.0153 (6)	−0.0054 (5)	−0.0046 (5)	0.0023 (5)
C2	0.0164 (6)	0.0104 (6)	0.0201 (7)	−0.0044 (5)	−0.0071 (5)	0.0015 (5)
O5A	0.068 (4)	0.0272 (17)	0.029 (2)	−0.013 (3)	−0.028 (3)	−0.0019 (16)
O5B	0.065 (4)	0.0194 (14)	0.032 (3)	−0.008 (2)	−0.032 (3)	−0.0016 (16)

Geometric parameters (Å, º)

Cl1—O1	1.4413 (11)	N7—C8	1.3138 (17)
Cl1—O3	1.4426 (10)	N7—C5	1.3784 (16)
Cl1—O2	1.4437 (11)	N3—C2	1.3033 (18)
Cl1—O4	1.4480 (11)	N3—C4	1.3534 (16)
Cl2—O5A	1.410 (6)	N9—C8	1.3465 (17)
Cl2—O8	1.4293 (12)	N9—C4	1.3736 (17)
Cl2—O6	1.4483 (11)	N6—C6	1.3090 (18)
Cl2—O7	1.4511 (13)	C5—C4	1.3802 (18)
Cl2—O5B	1.483 (6)	C5—C6	1.4145 (19)
N1—C6	1.3605 (17)	O5A—O5B	0.592 (7)
N1—C2	1.3681 (17)
O1—Cl1—O3	109.82 (7)	C8—N7—C5	108.34 (11)
O1—Cl1—O2	109.39 (7)	C2—N3—C4	112.31 (11)
O3—Cl1—O2	109.11 (6)	C8—N9—C4	108.09 (11)
O1—Cl1—O4	109.38 (7)	N7—C5—C4	107.23 (11)
O3—Cl1—O4	109.56 (6)	N7—C5—C6	133.46 (12)
O2—Cl1—O4	109.57 (7)	C4—C5—C6	119.25 (12)
O5A—Cl2—O8	121.7 (2)	N7—C8—N9	109.88 (12)
O5A—Cl2—O6	107.8 (3)	N3—C4—N9	126.97 (12)
O8—Cl2—O6	109.12 (7)	N3—C4—C5	126.55 (12)
O5A—Cl2—O7	99.8 (2)	N9—C4—C5	106.45 (11)
O8—Cl2—O7	108.92 (7)	N6—C6—N1	122.11 (13)
O6—Cl2—O7	108.68 (8)	N6—C6—C5	125.55 (13)
O5A—Cl2—O5B	23.4 (3)	N1—C6—C5	112.34 (12)
O8—Cl2—O5B	100.2 (2)	N3—C2—N1	125.09 (13)
O6—Cl2—O5B	110.7 (3)	O5B—O5A—Cl2	85.3 (12)
O7—Cl2—O5B	118.7 (2)	O5A—O5B—Cl2	71.3 (11)
C6—N1—C2	124.11 (12)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O7^i	0.86	2.16	2.909 (2)	146
N1—H1···O6	0.86	2.46	3.025 (2)	124
N7—H7···O1W^ii	0.86	1.91	2.686 (2)	150
N7—H7···O2^iii	0.86	2.40	2.963 (2)	123
N9—H9···O4^iv	0.86	2.09	2.849 (2)	146
N9—H9···O3^v	0.86	2.33	2.868 (2)	121
N6—H6A···O7^i	0.86	2.22	2.941 (2)	141
N6—H6B···O1W^ii	0.86	1.97	2.799 (2)	161
O1W—H1W···O6	0.80 (1)	2.03 (1)	2.798 (2)	160 (2)
O1W—H2W···N3^vi	0.78 (1)	2.25 (2)	2.907 (2)	142 (2)
O1W—H2W···O1^vii	0.78 (1)	2.47 (2)	3.002 (2)	127 (2)

Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x+1, −y, −z+1; (iii) x+1, y−1, z; (iv) x+1, y, z; (v) −x+2, −y, −z; (vi) −x+1, −y+1, −z+1; (vii) x, y, z+1.