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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 67| Part 2| February 2011| Page o427
doi:10.1107/S1600536811001528

Adeninium perchlorate

Hoong-Kun Fun,a*‡ Jia Hao Goh,a§ Annada C. Maityb and Shyamaprosad Goswamib

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bDepartment of Chemistry, Bengal Engineering and Science University, Shibpur, Howrah 711 103, India
*Correspondence e-mail: hkfun@usm.my

(Received 24 December 2010; accepted 11 January 2011; online 15 January 2011)

In the title salt (systematic name: 6-amino-9H-purin-1-ium perchlorate), C5H6N5+·ClO4−, the adeninium cation is essentially planar, with a maximum deviation of 0.038 (1) Å. The whole of the perchlorate anion is disordered over two sets of sites with an occupancy ratio of 0.589 (13):0.411 (13). In the crystal, the adeninium cations are linked by pairs of N—H⋯N hydrogen bond into inversion dimers. The dimers and the anions are further inter­connected into a three-dimensional supra­molecular structure via inter­molecular N—H⋯O, C—H⋯O and C—H⋯N hydrogen bonds.

Related literature

For general background to and applications of the title adeninium salt, see: Biradha et al. (2010[Biradha, K., Samai, S., Maity, A. C. & Goswami, S. (2010). Cryst. Growth Des. 10, 937-942.]); Goswami et al. (2007[Goswami, S., Maity, A. C. & Fun, H.-K. (2007). Eur. J. Org. Chem. pp. 4056-4064.]). For a closely related adeninium structure, see: Zeleňák et al. (2004[Zeleňák, V., Vargová, Z. & Císařová, I. (2004). Acta Cryst. E60, o742-o744.]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data

  • C5H6N5+·ClO4−

  • Mr = 235.60

  • Monoclinic, P 21 /c

  • a = 8.7614 (2) Å

  • b = 4.8234 (1) Å

  • c = 21.0758 (4) Å

  • β = 112.070 (1)°

  • V = 825.39 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.47 mm−1

  • T = 105 K

  • 0.29 × 0.28 × 0.20 mm
Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.878, Tmax = 0.911

  • 13078 measured reflections

  • 3149 independent reflections

  • 2538 reflections with I > 2σ(I)

  • Rint = 0.037
Refinement

  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 0.101

  • S = 1.04

  • 3149 reflections

  • 200 parameters

  • 10 restraints

  • All H-atom parameters refined

  • Δρmax = 0.45 e Å−3

  • Δρmin = −0.42 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N1—H1N1⋯O3i 0.82 (2) 2.23 (2) 2.868 (7) 135.2 (17)
N3—H1N3⋯O4ii 0.79 (2) 2.07 (2) 2.818 (10) 158.2 (19)
N5—H1N5⋯N4iii 0.85 (2) 2.07 (2) 2.8938 (19) 164.3 (19)
N5—H2N5⋯O2i 0.85 (2) 2.28 (2) 3.100 (6) 162.0 (18)
C3—H3⋯N2iv 0.945 (19) 2.577 (19) 3.266 (2) 130.0 (15)
C3—H3⋯O1v 0.945 (19) 2.35 (2) 3.055 (6) 131.2 (16)
C5—H5⋯O4 0.94 (2) 2.45 (2) 3.174 (10) 133.6 (15)
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) [-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iii) -x+1, -y, -z+1; (iv) -x, -y+2, -z+1; (v) [x-1, -y+{\script{3\over 2}}, z-{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811001528/is2652sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811001528/is2652Isup2.hkl

checkCIF report


Comment top

Adenine is a purine derivative nucleobase. Adenine is probably one of the most widely-used nucleobase in biochemistry (Biradha et al., 2010). It is an integral part of DNA, RNA and ATP. As a nucleobase, adenine exhibits a tendency to self-associate with the help of Watson-Crick and Hoogsteen hydrogen bonds. We have recently reported the unique hydrogen bonding participation of H5O2+ bridging two hydrogen-bonded dimers of lumazine in its co-crystal with aqueous perchloric acid and the supramolecular assembly of protonated xanthine alkaloids in their perchlorate salts (Goswami et al., 2007). In the present work, we report the crystal structure of adenine perchlorate.

The title salt comprises a protonated 6-amino-9H-purin-1-ium cation and a perchlorate anion (Fig. 1). The 6-amino-9H-purin-1-ium cation (C1–C5/N1–N5) is essentially planar, as indicated by the maximum deviation of 0.038 (1) Å at atom C1. The whole molecule of perchlorate anion (Cl/O1–O4) is disordered over two sites with refined occupancies of 0.589 (13) and 0.411 (13). All geometric parameters are consistent to a reported adeninium structure (Zeleňák et al., 2004).

In the crystal packing, all hydrogen atoms take part in hydrogen bonding between the cation and anion. Intermolecular N1—H1N1···O3, N3—H1N3···O4, N5—H1N5···N4, N5—H2N5···O2, C3—H3···O1, C3—H3···N2 and C5—H5···O4 hydrogen bonds (Table 1) interconnect the ions into a three-dimensional supramolecular structure (Fig. 2).

Related literature top

For general background to and applications of the title adeninium salt, see: Biradha et al. (2010); Goswami et al. (2007). For a closely related adeninium structure, see: Zeleňák et al. (2004). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).

Experimental top

Adenine (150 mg) was dissolved in perchloric acid (70 %, 1.0 ml) with gentle warming and the reaction mixture was kept at room temperature. After several days, colourless single crystals were separated, which were collected and dried.

Refinement top

All H atoms were located in a difference Fourier map, and allowed to refine freely with C—H = 0.942 (19)–0.95 (2) Å and N—H = 0.79 (2)–0.85 (2) Å. The whole molecule of perchlorate anion is disordered over two sites with a refined occupancy ratio of 0.589 (13):0.411 (13). Similarity restraints were applied for the perchlorate anion.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title salt, showing 50% probability displacement ellipsoids for non-H atoms and the atom-numbering scheme. Minor disordered component is shown as open bonds and labelled as suffix X.
[Figure 2] Fig. 2. The crystal structure of the title salt, viewed along the b axis, showing a 3D supramolecular structure. Minor disordered component is omitted for clarity and intermolecular hydrogen bonds are shown as dashed lines.
6-amino-9H-purin-1-ium perchlorate top
Crystal data top
C5H6N5+·ClO4−F(000) = 480
Mr = 235.60Dx = 1.896 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4267 reflections
a = 8.7614 (2) Åθ = 3.8–33.0°
b = 4.8234 (1) ŵ = 0.47 mm−1
c = 21.0758 (4) ÅT = 105 K
β = 112.070 (1)°Block, colourless
V = 825.39 (3) Å30.29 × 0.28 × 0.20 mm
Z = 4
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer		3149 independent reflections
Radiation source: fine-focus sealed tube2538 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.037
ϕ and ω scansθmax = 33.2°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		h = −13→13
Tmin = 0.878, Tmax = 0.911k = −7→7
13078 measured reflectionsl = −30→32
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.101All H-atom parameters refined
S = 1.04 w = 1/[σ2(Fo2) + (0.043P)2 + 0.4566P]
where P = (Fo2 + 2Fc2)/3
3149 reflections(Δ/σ)max < 0.001
200 parametersΔρmax = 0.45 e Å−3
10 restraintsΔρmin = −0.42 e Å−3
Crystal data top
C5H6N5+·ClO4−V = 825.39 (3) Å3
Mr = 235.60Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.7614 (2) ŵ = 0.47 mm−1
b = 4.8234 (1) ÅT = 105 K
c = 21.0758 (4) Å0.29 × 0.28 × 0.20 mm
β = 112.070 (1)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer		3149 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		2538 reflections with I > 2σ(I)
Tmin = 0.878, Tmax = 0.911Rint = 0.037
13078 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.03910 restraints
wR(F2) = 0.101All H-atom parameters refined
S = 1.04Δρmax = 0.45 e Å−3
3149 reflectionsΔρmin = −0.42 e Å−3
200 parameters
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 105.0 (1)K.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
xyzUiso*/UeqOcc. (<1)
N10.14134 (14)0.5810 (3)0.41768 (6)0.0152 (2)
N20.14035 (14)0.7456 (3)0.52342 (6)0.0169 (2)
N30.33327 (15)0.4802 (3)0.61809 (6)0.0177 (2)
N40.43640 (13)0.1928 (3)0.56071 (6)0.0153 (2)
N50.30483 (15)0.2191 (3)0.40417 (6)0.0162 (2)
C10.32179 (15)0.3695 (3)0.51586 (7)0.0137 (2)
C20.25906 (15)0.3820 (3)0.44387 (7)0.0134 (2)
C30.08746 (17)0.7514 (3)0.45686 (7)0.0167 (3)
C40.25733 (16)0.5486 (3)0.55077 (7)0.0148 (2)
C50.43785 (16)0.2674 (3)0.62123 (7)0.0174 (3)
Cl10.7997 (9)0.4578 (14)0.7670 (3)0.0170 (6)0.589 (13)
O10.9452 (8)0.4076 (15)0.8255 (3)0.0317 (11)0.589 (13)
O20.7796 (6)0.7499 (5)0.7523 (3)0.0294 (9)0.589 (13)
O30.8120 (11)0.3197 (11)0.7080 (3)0.0183 (8)0.589 (13)
O40.6558 (10)0.359 (2)0.7785 (5)0.020 (2)0.589 (13)
Cl1X0.8150 (12)0.4603 (19)0.7747 (5)0.0155 (7)0.411 (13)
O1X0.9454 (11)0.3192 (15)0.8286 (5)0.0216 (11)0.411 (13)
O2X0.8317 (7)0.7552 (7)0.7882 (5)0.0285 (16)0.411 (13)
O3X0.8155 (16)0.398 (2)0.7091 (5)0.0242 (16)0.411 (13)
O4X0.6614 (13)0.362 (3)0.7772 (7)0.020 (3)0.411 (13)
H1N10.098 (2)0.598 (4)0.3760 (10)0.024*
H1N30.322 (2)0.554 (4)0.6494 (11)0.024*
H1N50.382 (3)0.103 (4)0.4224 (10)0.024*
H2N50.259 (2)0.223 (4)0.3606 (10)0.024*
H30.005 (2)0.880 (4)0.4324 (10)0.024*
H50.501 (2)0.182 (4)0.6632 (10)0.024*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0165 (5)0.0140 (6)0.0156 (5)0.0027 (4)0.0068 (4)0.0033 (4)
N20.0161 (5)0.0142 (6)0.0212 (5)0.0006 (5)0.0079 (4)−0.0016 (5)
N30.0183 (5)0.0202 (6)0.0150 (5)0.0007 (5)0.0068 (4)−0.0037 (5)
N40.0143 (5)0.0144 (5)0.0158 (5)0.0004 (4)0.0042 (4)0.0003 (4)
N50.0183 (5)0.0157 (6)0.0143 (5)0.0049 (5)0.0058 (4)0.0006 (4)
C10.0140 (5)0.0118 (6)0.0151 (5)−0.0008 (5)0.0053 (4)−0.0007 (5)
C20.0140 (5)0.0108 (6)0.0160 (5)−0.0001 (5)0.0065 (4)0.0012 (5)
C30.0168 (5)0.0121 (6)0.0227 (6)0.0013 (5)0.0091 (5)0.0017 (5)
C40.0149 (5)0.0122 (6)0.0176 (6)−0.0020 (5)0.0067 (4)−0.0022 (5)
C50.0159 (5)0.0190 (7)0.0161 (6)−0.0006 (5)0.0047 (4)−0.0008 (5)
Cl10.0164 (11)0.0164 (7)0.0169 (10)−0.0001 (6)0.0049 (8)0.0010 (5)
O10.0236 (13)0.050 (3)0.0164 (13)0.002 (2)0.0015 (9)0.003 (2)
O20.0461 (18)0.0134 (10)0.035 (2)−0.0033 (10)0.0222 (18)−0.0004 (10)
O30.0203 (13)0.020 (2)0.0154 (11)−0.0009 (18)0.0073 (9)0.0004 (14)
O40.016 (3)0.026 (4)0.024 (4)−0.007 (2)0.015 (3)−0.001 (3)
Cl1X0.0133 (13)0.0132 (9)0.021 (2)−0.0005 (8)0.0080 (15)0.0022 (11)
O1X0.0182 (16)0.026 (3)0.0145 (16)0.007 (2)−0.0008 (12)0.005 (2)
O2X0.033 (2)0.0076 (12)0.050 (4)−0.0005 (13)0.022 (2)−0.0003 (16)
O3X0.0252 (19)0.037 (4)0.0128 (17)−0.007 (4)0.0098 (13)0.003 (3)
O4X0.024 (5)0.022 (6)0.013 (4)0.005 (4)0.006 (3)0.007 (4)
Geometric parameters (Å, º) top
N1—C21.3646 (18)C1—C41.3855 (19)
N1—C31.3686 (18)C1—C21.4075 (18)
N1—H1N10.82 (2)C3—H30.95 (2)
N2—C31.3018 (18)C5—H50.942 (19)
N2—C41.3571 (18)Cl1—O11.423 (7)
N3—C51.361 (2)Cl1—O21.439 (7)
N3—C41.3620 (18)Cl1—O31.449 (7)
N3—H1N30.79 (2)Cl1—O41.450 (7)
N4—C51.3208 (18)Cl1X—O3X1.417 (10)
N4—C11.3837 (17)Cl1X—O1X1.443 (9)
N5—C21.3153 (18)Cl1X—O4X1.446 (10)
N5—H1N50.85 (2)Cl1X—O2X1.447 (9)
N5—H2N50.85 (2)
C2—N1—C3123.92 (12)N1—C3—H3115.6 (12)
C2—N1—H1N1118.7 (14)N2—C4—N3127.42 (13)
C3—N1—H1N1117.4 (14)N2—C4—C1127.20 (12)
C3—N2—C4112.27 (12)N3—C4—C1105.37 (12)
C5—N3—C4106.86 (12)N4—C5—N3113.36 (12)
C5—N3—H1N3126.2 (15)N4—C5—H5125.2 (12)
C4—N3—H1N3126.9 (15)N3—C5—H5121.4 (12)
C5—N4—C1103.49 (12)O1—Cl1—O2110.5 (5)
C2—N5—H1N5119.2 (13)O1—Cl1—O3109.5 (6)
C2—N5—H2N5122.7 (13)O2—Cl1—O3108.0 (5)
H1N5—N5—H2N5118.0 (18)O1—Cl1—O4110.6 (6)
N4—C1—C4110.93 (12)O2—Cl1—O4108.2 (6)
N4—C1—C2130.69 (12)O3—Cl1—O4110.0 (7)
C4—C1—C2118.28 (12)O3X—Cl1X—O1X112.0 (8)
N5—C2—N1121.84 (12)O3X—Cl1X—O4X108.0 (10)
N5—C2—C1124.83 (12)O1X—Cl1X—O4X106.8 (8)
N1—C2—C1113.32 (12)O3X—Cl1X—O2X111.3 (7)
N2—C3—N1125.00 (13)O1X—Cl1X—O2X108.5 (6)
N2—C3—H3119.4 (12)O4X—Cl1X—O2X110.0 (9)
C5—N4—C1—C40.39 (15)C3—N2—C4—N3−177.16 (14)
C5—N4—C1—C2−175.98 (14)C3—N2—C4—C11.0 (2)
C3—N1—C2—N5178.65 (13)C5—N3—C4—N2178.41 (14)
C3—N1—C2—C1−0.51 (19)C5—N3—C4—C1−0.11 (15)
N4—C1—C2—N5−1.6 (2)N4—C1—C4—N2−178.70 (13)
C4—C1—C2—N5−177.75 (13)C2—C1—C4—N2−1.8 (2)
N4—C1—C2—N1177.53 (13)N4—C1—C4—N3−0.17 (16)
C4—C1—C2—N11.38 (18)C2—C1—C4—N3176.70 (12)
C4—N2—C3—N10.0 (2)C1—N4—C5—N3−0.47 (16)
C2—N1—C3—N2−0.2 (2)C4—N3—C5—N40.38 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O3i0.82 (2)2.23 (2)2.868 (7)135.2 (17)
N3—H1N3···O4ii0.79 (2)2.07 (2)2.818 (10)158.2 (19)
N5—H1N5···N4iii0.85 (2)2.07 (2)2.8938 (19)164.3 (19)
N5—H2N5···O2i0.85 (2)2.28 (2)3.100 (6)162.0 (18)
C3—H3···N2iv0.945 (19)2.577 (19)3.266 (2)130.0 (15)
C3—H3···O1v0.945 (19)2.35 (2)3.055 (6)131.2 (16)
C5—H5···O40.94 (2)2.45 (2)3.174 (10)133.6 (15)
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1, y+1/2, −z+3/2; (iii) −x+1, −y, −z+1; (iv) −x, −y+2, −z+1; (v) x−1, −y+3/2, z−1/2.

Experimental details

Crystal data
Chemical formulaC5H6N5+·ClO4−
Mr235.60
Crystal system, space groupMonoclinic, P21/c
Temperature (K)105
a, b, c (Å)8.7614 (2), 4.8234 (1), 21.0758 (4)
β (°) 112.070 (1)
V (Å3)825.39 (3)
Z4
Radiation typeMo Kα
µ (mm−1)0.47
Crystal size (mm)0.29 × 0.28 × 0.20
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.878, 0.911
No. of measured, independent and
observed [I > 2σ(I)] reflections		13078, 3149, 2538
Rint0.037
(sin θ/λ)max (Å−1)0.770
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.101, 1.04
No. of reflections3149
No. of parameters200
No. of restraints10
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å−3)0.45, −0.42

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N1···O3i0.82 (2)2.23 (2)2.868 (7)135.2 (17)
N3—H1N3···O4ii0.79 (2)2.07 (2)2.818 (10)158.2 (19)
N5—H1N5···N4iii0.85 (2)2.07 (2)2.8938 (19)164.3 (19)
N5—H2N5···O2i0.85 (2)2.28 (2)3.100 (6)162.0 (18)
C3—H3···N2iv0.945 (19)2.577 (19)3.266 (2)130.0 (15)
C3—H3···O1v0.945 (19)2.35 (2)3.055 (6)131.2 (16)
C5—H5···O40.94 (2)2.45 (2)3.174 (10)133.6 (15)
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1, y+1/2, −z+3/2; (iii) −x+1, −y, −z+1; (iv) −x, −y+2, −z+1; (v) x−1, −y+3/2, z−1/2.
 

Footnotes

‡Thomson Reuters ResearcherID: A-3561-2009.

§Thomson Reuters ResearcherID: C-7576-2009.

Acknowledgements

HKF and JHG thank Universiti Sains Malaysia for the Research University Grant (No. 1001/PFIZIK/811160). ACM and SG thank the DST [SR/S1/OC-13/2005], Government of India, for financial support. ACM also thanks the UGC, Government of India, for a fellowship.

References

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ISSN: 2056-9890
Volume 67| Part 2| February 2011| Page o427
doi:10.1107/S1600536811001528
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