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Redetermination of adeninium di­chloride: the question of centrosymmetry

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aDepartment of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England
*Correspondence e-mail: d.a.tocher@ucl.ac.uk

(Received 7 March 2005; accepted 14 March 2005; online 25 March 2005)

The low-temperature redetermination of adeninium(2+) dichloride, C5H7N52+·2Cl, obtained as part of an experimental polymorph screen on adenine, is reported here. The crystal structure is shown to be centrosymmetric. Cations and anions are connected through N—H⋯N and N—H⋯Cl hydrogen bonds [N⋯N = 2.899 (2) Å and N⋯Cl = 3.0274 (14)–3.5155 (16) Å] to form sheets perpendicular to the b axis.

Comment

The title compound, (I[link]), is a hydro­chloride salt of adenine, which is one of the two common purine bases found in ribose and deoxy­ribose nucleic acids. [link]

[Scheme 1]

The unit cell was determined in 1974 (Iwasaki, 1974[Iwasaki, H. (1974). Chem. Lett. 5, 409-410.]); however, it was not possible unequivocally to establish the correct space group, either Pna21 or Pnam (non-standard setting of Pnma), as refinement in each gave similar R values (0.043 and 0.045, respectively). The structure was also determined at room temperature by Kistenmacher & Shigematsu (1974[Kistenmacher, T. J. & Shigematsu, T. (1974). Acta Cryst. B30, 1528-1533.]), and refined in the centrosymmetric space group Pnma, giving an R value of 0.035. In this space group, mirror symmetry is imposed on the adenine dication, with some atoms having large r.m.s. displacements normal to the mirror plane. However, it was argued that purines commonly show some bending about the C2—C3 bond axis (Sletten & Jessen, 1969[Sletten, J. & Jessen, L. H. (1969). Acta Cryst. B25, 1608-1614.]), which is inconsistent with the analysis in the centrosymmetric space group. Hence, it was suggested that the true space group could be Pn21a (non-standard setting of Pna21).We have redetermined the crystal structure at 150 K, to gain more precise data for our molecular modelling studies. The structure was refined in both Pnma and Pna21, giving R values of 0.0241 and 0.0229, respectively, despite the statistical averages for the normalized structure factors (E values) being more consistent with a centrosymmetric than a non-centro­symmetric distribution. However, when refined in the non-centrosymmetric space group, all the ring H atoms deviate by between 13–15° from the mean ring plane to which they are attached. These are large deviations when compared with other adeninium crystal structures, which include adeninium sulfate (Langer & Huml, 1978[Langer, V. & Huml, K. (1978). Acta Cryst. B34, 1157-1163.]), adeninium dinitrate (Hardgrove et al., 1983[Hardgrove, G. L Jr, Einstein, J. R. Hingerty, B. E. & Wei, C. H. (1983). Acta Cryst. C39, 88-90.]) and adeninium diperchlorate monohydrate (Bendjeddou et al., 2003[Bendjeddou, L., Cherouana, A., Dahaoui, S., Benali-Cherif, N. & Lecomte, C. (2003). Acta Cryst. E59, o649-o651.]). In addition, analysing the non-centro­symmetric structure with PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]) to search for missing or higher symmetry gave the centrosymmetric structure at 100% confidence level. Hence, using the superior low-temperature data, we can conclude that the most likely space group of (I[link]) is Pnma.

In this low-temperature determination, the precision of the unit-cell dimensions was improved by an order of magnitude, and the unit-cell volume decreased by ca 14 Å3, consistent with the determination at low temperature. In general, the metric parameters are not significantly different, within standard deviations, from those found at room temperature. The adenine mol­ecule is protonated at N1 and N3, with the C—N bond lengths in the rings in the range 1.308 (2)–1.375 (2) Å, and the C2—C3, C3—C4 and C4—N5 bond lengths being 1.379 (2), 1.409 (2) and 1.310 (2) Å, respectively. In the crystal structure, the cations are linked through N—H⋯N hydrogen bonds to form extended chains in the a-axis direction. These chains are, in turn, linked by N—H⋯Cl hydrogen bonds to form sheets (Fig. 2[link]) lying parallel to the (040) family of lattice planes. Four of the H atoms on the adenine cation are involved in N—H⋯Cl hydrogen bonds (see Table 1[link]) and, in addition, atoms H4 and H6 are involved in weaker bifurcated N—H⋯Cl hydrogen bonds, with N⋯Cl distances of 3.2936 (15) and 3.5155 (16) Å, respectively. There are two independent Cl ions within the hydrogen-bonded sheets: Cl1, which is involved in one conventional and three weaker bifurcated N—H⋯Cl hydrogen bonds, and Cl2, which is involved in three conventional N—H⋯Cl hydrogen bonds. In the N—H⋯N and N—H⋯Cl hydrogen-bonded sheets, all acceptors and donors are used.

[Figure 1]
Figure 1
View of (I[link]), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2]
Figure 2
View of the hydrogen-bonded sheet motif present in (I[link]), with the hydrogen bonds shown as dotted lines; DA distances greater than 3.3 Å have been omitted for clarity.

Experimental

As part of an experimental polymorph screen on adenine, (I[link]) was obtained by evaporation of a solution of equimolecular amounts of thymine/adenine, and cytosine/adenine in dilute hydro­chloric acid, giving colourless block-shaped crystals.

Crystal data
  • C5H7N52+·2Cl

  • Mr = 208.06

  • Orthorhombic, Pnma

  • a = 13.4405 (11) Å

  • b = 6.4774 (5) Å

  • c = 9.3684 (7) Å

  • V = 815.61 (11) Å3

  • Z = 4

  • Dx = 1.694 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 5209 reflections

  • θ = 2.7–28.1°

  • μ = 0.74 mm−1

  • T = 150 (2) K

  • Block, colourless

  • 0.74 × 0.26 × 0.24 mm

Data collection
  • Bruker SMART APEX diffractometer

  • Narrow-frame ω scans

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.609, Tmax = 0.842

  • 6736 measured reflections

  • 1076 independent reflections

  • 1064 reflections with I > 2σ(I)

  • Rint = 0.016

  • θmax = 28.3°

  • h = −17 → 17

  • k = −8 → 8

  • l = −12 → 12

Refinement
  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.024

  • wR(F2) = 0.063

  • S = 0.99

  • 1076 reflections

  • 94 parameters

  • All H-atom parameters refined

  • w = 1/[σ2(Fo2) + (0.0337P)2 + 0.5379P] where P = (Fo2 + 2Fc2)/3

  • (Δ/σ)max < 0.001

  • Δρmax = 0.37 e Å−3

  • Δρmin = −0.25 e Å−3

Table 1
Hydrogen-bonding geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H2⋯Cl1 0.94 (3) 2.11 (3) 3.0274 (14) 167 (2)
N3—H3⋯Cl2i 0.89 (3) 2.25 (3) 3.0693 (14) 153 (2)
N4—H4⋯Cl1ii 0.90 (2) 2.53 (2) 3.2936 (15) 143.8 (19)
N4—H4⋯Cl2ii 0.90 (2) 2.56 (2) 3.1695 (14) 126.1 (18)
N5—H6⋯N2iii 0.85 (2) 2.28 (2) 2.899 (2) 129.6 (19)
N5—H6⋯Cl1 0.85 (2) 2.82 (2) 3.5155 (16) 140.3 (18)
N5—H7⋯Cl2i 0.88 (3) 2.22 (3) 3.0985 (16) 175 (2)
Symmetry codes: (i) x,y,1+z; (ii) [{\script{1\over 2}}+x,y,{\script{3\over 2}}-z]; (iii) [x-{\script{1\over 2}},y,{\script{3\over 2}}-z].

H atoms were refined independently using an isotropic model.

Data collection: SMART (Bruker, 2000[Bruker (2000). SMART, SAINT and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SMART, SAINT and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990[Sheldrick, G. M. (1990). Acta Cryst. A46, 467-473.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany.]); molecular graphics: SHELXTL (Bruker, 2000[Bruker (2000). SMART, SAINT and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.]) and MERCURY (Bruno et al., 2002[Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M. K., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389-397.]); software used to prepare material for publication: SHELXL97.

Supporting information


Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2000) and Mercury (Bruno, 2002); software used to prepare material for publication: SHELXL97.

Adeninium(2+) dichloride top
Crystal data top
C5H7N52+·2ClF(000) = 424
Mr = 208.06Dx = 1.694 Mg m3
Orthorhombic, PnmaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2nCell parameters from 5209 reflections
a = 13.4405 (11) Åθ = 2.7–28.1°
b = 6.4774 (5) ŵ = 0.74 mm1
c = 9.3684 (7) ÅT = 150 K
V = 815.61 (11) Å3Block, colourless
Z = 40.74 × 0.26 × 0.24 mm
Data collection top
Bruker SMART APEX
diffractometer
1076 independent reflections
Radiation source: fine-focus sealed tube1064 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.016
ω rotation scans with narrow framesθmax = 28.3°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 1717
Tmin = 0.609, Tmax = 0.842k = 88
6736 measured reflectionsl = 1212
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)] = 0.024Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.063All H-atom parameters refined
S = 0.99 w = 1/[σ2(Fo2) + (0.0337P)2 + 0.5379P]
where P = (Fo2 + 2Fc2)/3
1076 reflections(Δ/σ)max < 0.001
94 parametersΔρmax = 0.37 e Å3
0 restraintsΔρmin = 0.25 e Å3
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
xyzUiso*/Ueq
Cl10.19853 (3)0.25000.44260 (4)0.02093 (12)
Cl20.06411 (3)0.25000.11040 (4)0.02752 (14)
N10.32438 (10)0.25000.71060 (15)0.0199 (3)
N20.47861 (10)0.25000.83213 (15)0.0216 (3)
N30.29232 (10)0.25001.09822 (14)0.0180 (3)
N40.45453 (10)0.25001.09002 (15)0.0187 (3)
N50.16825 (10)0.25000.81532 (16)0.0233 (3)
C10.42539 (12)0.25000.71522 (18)0.0225 (3)
C20.42189 (11)0.25000.95093 (16)0.0163 (3)
C30.31936 (11)0.25000.95674 (17)0.0164 (3)
C40.26529 (12)0.25000.82791 (16)0.0172 (3)
C50.37495 (12)0.25001.17584 (17)0.0199 (3)
H10.4584 (17)0.25000.631 (2)0.026 (5)*
H20.2946 (18)0.25000.620 (3)0.034 (6)*
H30.231 (2)0.25001.133 (3)0.042 (7)*
H40.5164 (18)0.25001.125 (2)0.026 (6)*
H50.3745 (14)0.25001.277 (2)0.018 (5)*
H60.1424 (16)0.25000.733 (3)0.022 (5)*
H70.1355 (17)0.25000.896 (3)0.033 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0201 (2)0.0261 (2)0.0166 (2)0.0000.00298 (13)0.000
Cl20.0153 (2)0.0514 (3)0.0159 (2)0.0000.00137 (13)0.000
N10.0170 (6)0.0298 (7)0.0129 (6)0.0000.0016 (5)0.000
N20.0144 (6)0.0323 (8)0.0179 (7)0.0000.0012 (5)0.000
N30.0145 (6)0.0264 (7)0.0130 (6)0.0000.0004 (5)0.000
N40.0140 (6)0.0261 (7)0.0159 (6)0.0000.0024 (5)0.000
N50.0145 (6)0.0406 (9)0.0150 (7)0.0000.0034 (5)0.000
C10.0175 (8)0.0351 (9)0.0150 (7)0.0000.0024 (6)0.000
C20.0148 (7)0.0197 (7)0.0145 (7)0.0000.0015 (5)0.000
C30.0148 (7)0.0202 (7)0.0142 (7)0.0000.0000 (5)0.000
C40.0160 (7)0.0211 (7)0.0146 (7)0.0000.0009 (5)0.000
C50.0174 (7)0.0261 (8)0.0161 (7)0.0000.0007 (6)0.000
Geometric parameters (Å, º) top
N1—C41.356 (2)N4—C21.375 (2)
N1—C11.358 (2)N4—H40.90 (2)
N1—H20.94 (3)N5—C41.310 (2)
N2—C11.308 (2)N5—H60.85 (2)
N2—C21.349 (2)N5—H70.88 (3)
N3—C51.327 (2)C1—H10.91 (2)
N3—C31.374 (2)C2—C31.379 (2)
N3—H30.89 (3)C3—C41.409 (2)
N4—C51.338 (2)C5—H50.95 (2)
C4—N1—C1124.03 (15)N2—C1—H1117.5 (14)
C4—N1—H2118.9 (15)N1—C1—H1117.5 (14)
C1—N1—H2117.1 (15)N2—C2—N4126.98 (14)
C1—N2—C2112.44 (13)N2—C2—C3126.67 (14)
C5—N3—C3107.88 (14)N4—C2—C3106.35 (14)
C5—N3—H3125.3 (17)N3—C3—C2107.60 (14)
C3—N3—H3126.9 (17)N3—C3—C4133.61 (15)
C5—N4—C2108.32 (13)C2—C3—C4118.80 (14)
C5—N4—H4121.5 (14)N5—C4—N1120.68 (15)
C2—N4—H4130.2 (14)N5—C4—C3126.22 (15)
C4—N5—H6119.3 (14)N1—C4—C3113.09 (13)
C4—N5—H7114.9 (15)N3—C5—N4109.86 (14)
H6—N5—H7126 (2)N3—C5—H5122.9 (11)
N2—C1—N1124.98 (16)N4—C5—H5127.3 (11)
C2—N2—C1—N10.0N2—C2—C3—C40.0
C4—N1—C1—N20.0N4—C2—C3—C4180.0
C1—N2—C2—N4180.0C1—N1—C4—N5180.0
C1—N2—C2—C30.0C1—N1—C4—C30.0
C5—N4—C2—N2180.0N3—C3—C4—N50.0
C5—N4—C2—C30.0C2—C3—C4—N5180.0
C5—N3—C3—C20.0N3—C3—C4—N1180.0
C5—N3—C3—C4180.0C2—C3—C4—N10.0
N2—C2—C3—N3180.0C3—N3—C5—N40.0
N4—C2—C3—N30.0C2—N4—C5—N30.0
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H2···Cl10.94 (3)2.11 (3)3.0274 (14)167 (2)
N3—H3···Cl2i0.89 (3)2.25 (3)3.0693 (14)153 (2)
N4—H4···Cl1ii0.90 (2)2.53 (2)3.2936 (15)144 (2)
N4—H4···Cl2ii0.90 (2)2.56 (2)3.1695 (14)126 (2)
N5—H6···N2iii0.85 (2)2.28 (2)2.899 (2)130 (2)
N5—H6···Cl10.85 (2)2.82 (2)3.5155 (16)140 (2)
N5—H7···Cl2i0.88 (3)2.22 (3)3.0985 (16)175 (2)
Symmetry codes: (i) x, y, z+1; (ii) x+1/2, y, z+3/2; (iii) x1/2, y, z+3/2.
 

Acknowledgements

This research was supported by the EPSRC in funding a studentship for TCL. The authors acknowledge the Research Councils UK Basic Technology Programme for supporting `Control and Prediction of the Organic Solid State'. For more information on this work, please visit https://www.cposs.org.uk.

References

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