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

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ISSN: 2056-9890

Redetermination of guaninium chloride dihydrate

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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 25 February 2005; accepted 9 March 2005; online 18 March 2005)

The low-temperature redetermination of guaninium chloride dihydrate, C5H6N5O+·Cl·2H2O, obtained as part of an experimental polymorph screen on guanine, is reported here.

Comment

The title compound, (I[link]), is a dihydrate salt of guanine, which is one of the two common purine bases found in ribose and deoxyribonucleic acids. The unit cell and space group of (I[link]) were originally reported in 1951 (Broomhead, 1951[Broomhead, J. (1951). Acta Cryst. 4, 92-100.]), with a room-temperature X-ray determination performed 12 years later (Iball & Wilson, 1963[Iball, J. & Wilson, H. R. (1963). Nature (London), 4886, 1193-1195.], 1965[Iball, J. & Wilson, H. R. (1965). Proc. R. Soc. London Ser. A, 288, 418-439.]). In this original determination, the intensities were recorded using Weissenberg photographs. All the atoms, including H atoms, were located by means of a difference Fourier synthesis and the structure refined to a final R value of 0.073. We have redetermined this crystal structure at 150 K, with a final R value of 0.032, to gain more precise data for our theoretical modelling studies.[link]

[Scheme 1]

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, the exception being the C1—N2 bond length which is longer in the low-temperature structure, while C1—N5 is shorter in the low-temperature structure, both by ca 0.03 Å. The guanine mol­ecule is protonated at N1 and N4, with the C—N bond lengths in the rings ranging from 1.3154 (18) to 1.3892 (18) Å, and the C2—C3, C3—C4 and N5—C1 bond lengths being 1.3797 (18), 1.4202 (19) and 1.3291 (18) Å, respectively.

The packing consists of centrosymmetric dimers, the two components of which are linked by pairs of N—H⋯N hydrogen bonds. These dimers are linked to four water mol­ecules and two Cl atoms to form a planar unit (Fig. 2[link]). These planar units are linked to one another through O—H⋯Cl hydrogen bonds within the plane, forming a ribbon structure, and through N—H⋯Cl and N—H⋯O hydrogen bonds at an angle of approximately 80° from this plane, forming a complex three-dimensional hydrogen-bonded network (Fig. 3[link]). The two H atoms on the NH2 group form two very dissimilar hydrogen bonds. A strong bond [N5—H7⋯N2iv = 3.0162 (17) Å; see Table 1[link]] is formed by one, while the second [N5—H6⋯Cl1i = 3.4368 (15) Å; see Table 1[link]] is weak.The N—H⋯N distance within the centrosymmetric dimer is 3.0162 (17) Å, with the N—H⋯O distances ranging from 2.6463 (17) to 3.0348 (17) Å. The N—H⋯Cl distances are 3.1281 (13) and 3.4368 (15) Å, and the O—H⋯Cl distances range from 3.1173 (14) to 3.1576 (13) Å. The O—H⋯O hydrogen bond involving the carbonyl group is 2.7404 (15) Å.

[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
The hydrogen-bonded (dashed lines) planar unit in (I[link]), showing the centrosymmetric dimer linked to four water mol­ecules and two Cl ions. The other hydrogen bonds have been omitted for clarity.
[Figure 3]
Figure 3
The crystal packing of (I[link]), showing the complex three-dimensional hydrogen-bonding network (dashed lines).

Experimental

As part of an experimental polymorph screen on guanine, (I[link]) was obtained from a solution of guanine in dilute hydro­chloric acid which was allowed to evaporate at room temperature (10 ml solution, in 75 × 25 mm vessels), forming block-shaped crystals. If the same guanine solution in dilute hydro­chloric acid was allowed to evaporate at a slower rate by virtue of a smaller surface area, small block-like crystals of guaninium chloride monohydrate were obtained.

Crystal data
  • C5H6N5O+·Cl·2H2O

  • Mr = 223.63

  • Monoclinic, P21/c

  • a = 4.8587 (11) Å

  • b = 13.228 (3) Å

  • c = 14.612 (3) Å

  • β = 93.862 (4)°

  • V = 937.0 (4) Å3

  • Z = 4

  • Dx = 1.585 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 2645 reflections

  • θ = 2.1–28.2°

  • μ = 0.40 mm−1

  • T = 150 (2) K

  • Block, colourless

  • 0.42 × 0.12 × 0.08 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 = 0.850, Tmax = 0.969

  • 7902 measured reflections

  • 2230 independent reflections

  • 1891 reflections with I > 2σ(I)

  • Rint = 0.024

  • θmax = 28.2°

  • h = −6 → 6

  • k = −17 → 17

  • l = −19 → 19

Refinement
  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 0.082

  • S = 1.04

  • 2230 reflections

  • 167 parameters

  • All H-atom parameters refined

  • w = 1/[σ2(Fo2) + (0.0433P)2 + 0.2271P] where P = (Fo2 + 2Fc2)/3

  • (Δ/σ)max = 0.001

  • Δρmax = 0.34 e Å−3

  • Δρmin = −0.19 e Å−3

Table 1
Hydrogen-bonding geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯Cl1i 0.883 (18) 2.261 (19) 3.1281 (13) 167.2 (16)
N3—H3⋯O1Wii 0.87 (2) 1.83 (2) 2.6867 (16) 167.8 (19)
N4—H4⋯O2W 0.908 (19) 1.76 (2) 2.6463 (17) 164.2 (18)
N5—H6⋯O1Wiii 0.861 (18) 2.518 (17) 3.0348 (17) 119.5 (13)
N5—H6⋯Cl1i 0.861 (18) 2.682 (18) 3.4368 (15) 147.2 (14)
N5—H7⋯N2iv 0.886 (19) 2.131 (19) 3.0162 (17) 176.9 (17)
O2W—H3W⋯Cl1 0.81 (2) 2.36 (2) 3.1576 (13) 167.9 (19)
O2W—H4W⋯Cl1v 0.85 (2) 2.27 (2) 3.1173 (14) 169.2 (19)
O1W—H1W⋯Cl1 0.85 (2) 2.31 (2) 3.1336 (13) 166.0 (17)
O1W—H2W⋯O4 0.85 (2) 1.93 (2) 2.7404 (15) 160 (2)
Symmetry codes: (i) [1-x,y-{\script{1\over 2}},{\script{1\over 2}}-z]; (ii) [x-1,{\script{3\over 2}}-y,{\script{1\over 2}}+z]; (iii) [-x,y-{\script{1\over 2}},{\script{1\over 2}}-z]; (iv) -1-x,1-y,1-z; (v) 2-x,2-y,1-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: BSAINT (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 et al., 2002); software used to prepare material for publication: SHELXL97.

Guaninium chloride dihydrate top
Crystal data top
C5H6N5O+·Cl·2H2OF(000) = 464
Mr = 223.63Dx = 1.585 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 4.8587 (11) ÅCell parameters from 2645 reflections
b = 13.228 (3) Åθ = 2.1–28.2°
c = 14.612 (3) ŵ = 0.40 mm1
β = 93.862 (4)°T = 150 K
V = 937.0 (4) Å3Block, colourless
Z = 40.42 × 0.12 × 0.08 mm
Data collection top
Bruker SMART APEX
diffractometer
2230 independent reflections
Radiation source: fine-focus sealed tube1891 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
ω rotation scans with narrow framesθmax = 28.2°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 66
Tmin = 0.850, Tmax = 0.969k = 1717
7902 measured reflectionsl = 1919
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)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.082All H-atom parameters refined
S = 1.04 w = 1/[σ2(Fo2) + (0.0433P)2 + 0.2271P]
where P = (Fo2 + 2Fc2)/3
2230 reflections(Δ/σ)max = 0.001
167 parametersΔρmax = 0.34 e Å3
0 restraintsΔρmin = 0.19 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
Cl11.11784 (8)0.97938 (3)0.33430 (2)0.02731 (12)
O40.3146 (2)0.70459 (7)0.30721 (7)0.0229 (2)
O1W0.6924 (2)0.83072 (9)0.23556 (7)0.0255 (2)
O2W0.7162 (2)0.90818 (9)0.48276 (9)0.0284 (3)
N10.0342 (2)0.60277 (9)0.34807 (8)0.0180 (2)
N20.2267 (2)0.59985 (8)0.49343 (7)0.0180 (2)
N30.0027 (2)0.72248 (9)0.59658 (8)0.0196 (3)
N40.2943 (2)0.78712 (9)0.50781 (8)0.0192 (2)
N50.3795 (3)0.49067 (9)0.37818 (9)0.0214 (3)
C10.2146 (3)0.56538 (10)0.40844 (9)0.0170 (3)
C20.0421 (3)0.67400 (10)0.51360 (9)0.0171 (3)
C30.1454 (3)0.71508 (10)0.45727 (9)0.0172 (3)
C40.1597 (3)0.67858 (10)0.36631 (9)0.0177 (3)
C50.2011 (3)0.78988 (11)0.59023 (9)0.0209 (3)
H10.036 (4)0.5739 (13)0.2936 (13)0.032 (5)*
H30.095 (4)0.7137 (14)0.6449 (15)0.041 (5)*
H40.429 (4)0.8279 (14)0.4882 (13)0.037 (5)*
H50.268 (3)0.8347 (13)0.6416 (12)0.025 (4)*
H60.373 (3)0.4697 (13)0.3226 (13)0.024 (4)*
H70.500 (4)0.4649 (13)0.4145 (12)0.030 (5)*
H3W0.798 (4)0.9297 (15)0.4400 (14)0.040 (6)*
H4W0.747 (4)0.9454 (16)0.5301 (16)0.044 (6)*
H1W0.795 (4)0.8675 (16)0.2709 (13)0.038 (5)*
H2W0.585 (5)0.7996 (17)0.2697 (16)0.053 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0360 (2)0.0291 (2)0.01704 (18)0.00440 (15)0.00350 (14)0.00212 (13)
O40.0246 (5)0.0255 (5)0.0198 (5)0.0048 (4)0.0099 (4)0.0002 (4)
O1W0.0278 (6)0.0296 (6)0.0200 (5)0.0062 (5)0.0088 (4)0.0019 (4)
O2W0.0274 (6)0.0339 (6)0.0244 (6)0.0098 (5)0.0061 (4)0.0052 (5)
N10.0195 (6)0.0197 (6)0.0154 (6)0.0012 (4)0.0049 (4)0.0013 (4)
N20.0189 (5)0.0184 (6)0.0173 (6)0.0006 (4)0.0056 (4)0.0006 (4)
N30.0228 (6)0.0210 (6)0.0156 (6)0.0011 (5)0.0056 (5)0.0007 (4)
N40.0190 (6)0.0197 (6)0.0193 (6)0.0010 (5)0.0034 (4)0.0012 (4)
N50.0225 (6)0.0226 (6)0.0198 (6)0.0049 (5)0.0069 (5)0.0022 (5)
C10.0165 (6)0.0165 (6)0.0183 (6)0.0026 (5)0.0039 (5)0.0024 (5)
C20.0180 (6)0.0172 (6)0.0164 (6)0.0035 (5)0.0042 (5)0.0009 (5)
C30.0166 (6)0.0171 (6)0.0182 (6)0.0006 (5)0.0032 (5)0.0007 (5)
C40.0181 (6)0.0176 (6)0.0177 (6)0.0019 (5)0.0042 (5)0.0019 (5)
C50.0226 (7)0.0209 (7)0.0194 (7)0.0025 (5)0.0020 (5)0.0017 (5)
Geometric parameters (Å, º) top
O4—C41.2321 (16)N3—C21.3736 (18)
O1W—H1W0.85 (2)N3—H30.87 (2)
O1W—H2W0.85 (2)N4—C51.3154 (18)
O2W—H3W0.81 (2)N4—C31.3802 (18)
O2W—H4W0.85 (2)N4—H40.908 (19)
N1—C11.3769 (17)N5—C11.3291 (18)
N1—C41.3892 (18)N5—H60.861 (18)
N1—H10.883 (18)N5—H70.886 (19)
N2—C11.3278 (18)C2—C31.3797 (18)
N2—C21.3481 (17)C3—C41.4202 (19)
N3—C51.3405 (19)C5—H50.995 (17)
H1W—O1W—H2W106.1 (19)N2—C1—N5120.19 (12)
H3W—O2W—H4W110.7 (19)N2—C1—N1123.09 (12)
C1—N1—C4126.10 (12)N5—C1—N1116.72 (12)
C1—N1—H1117.0 (12)N2—C2—N3125.72 (12)
C4—N1—H1116.8 (12)N2—C2—C3127.75 (12)
C1—N2—C2112.57 (11)N3—C2—C3106.52 (12)
C5—N3—C2108.01 (12)C2—C3—N4107.22 (12)
C5—N3—H3124.6 (13)C2—C3—C4120.02 (12)
C2—N3—H3127.4 (13)N4—C3—C4132.73 (12)
C5—N4—C3107.99 (12)O4—C4—N1120.35 (12)
C5—N4—H4124.9 (12)O4—C4—C3129.18 (13)
C3—N4—H4127.1 (12)N1—C4—C3110.47 (11)
C1—N5—H6119.5 (11)N4—C5—N3110.26 (12)
C1—N5—H7119.8 (11)N4—C5—H5126.3 (10)
H6—N5—H7120.6 (16)N3—C5—H5123.5 (9)
C2—N2—C1—N5178.71 (12)N3—C2—C3—C4178.63 (11)
C2—N2—C1—N10.62 (18)C5—N4—C3—C20.28 (15)
C4—N1—C1—N21.1 (2)C5—N4—C3—C4178.36 (14)
C4—N1—C1—N5178.29 (12)C1—N1—C4—O4178.54 (12)
C1—N2—C2—N3178.52 (12)C1—N1—C4—C30.98 (18)
C1—N2—C2—C30.35 (19)C2—C3—C4—O4178.82 (13)
C5—N3—C2—N2178.93 (13)N4—C3—C4—O40.9 (3)
C5—N3—C2—C30.14 (15)C2—C3—C4—N10.65 (17)
N2—C2—C3—N4178.79 (13)N4—C3—C4—N1178.53 (14)
N3—C2—C3—N40.25 (14)C3—N4—C5—N30.19 (16)
N2—C2—C3—C40.4 (2)C2—N3—C5—N40.03 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···Cl1i0.883 (18)2.261 (19)3.1281 (13)167.2 (16)
N3—H3···O1Wii0.87 (2)1.83 (2)2.6867 (16)167.8 (19)
N4—H4···O2W0.908 (19)1.76 (2)2.6463 (17)164.2 (18)
N5—H6···O1Wiii0.861 (18)2.518 (17)3.0348 (17)119.5 (13)
N5—H6···Cl1i0.861 (18)2.682 (18)3.4368 (15)147.2 (14)
N5—H7···N2iv0.886 (19)2.131 (19)3.0162 (17)176.9 (17)
O2W—H3W···Cl10.81 (2)2.36 (2)3.1576 (13)167.9 (19)
O2W—H4W···Cl1v0.85 (2)2.27 (2)3.1173 (14)169.2 (19)
O1W—H1W···Cl10.85 (2)2.31 (2)3.1336 (13)166.0 (17)
O1W—H2W···O40.85 (2)1.93 (2)2.7404 (15)160 (2)
Symmetry codes: (i) x+1, y1/2, z+1/2; (ii) x1, y+3/2, z+1/2; (iii) x, y1/2, z+1/2; (iv) x1, y+1, z+1; (v) x+2, y+2, z+1.
 

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

First citationBroomhead, J. (1951). Acta Cryst. 4, 92–100.  CrossRef IUCr Journals Google Scholar
First citationBruker (2000). SMART, SAINT and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruno, 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.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationIball, J. & Wilson, H. R. (1963). Nature (London), 4886, 1193–1195.  Google Scholar
First citationIball, J. & Wilson, H. R. (1965). Proc. R. Soc. London Ser. A, 288, 418–439.  Google Scholar
First citationSheldrick, G. M. (1990). Acta Cryst. A46, 467–473.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany.  Google Scholar

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