Redetermination of guaninium chloride dihydrate

Lewis, T.C.; Tocher, D.A.

doi:10.1107/S160053680500752X

organic compounds

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Volume 61| Part 4| April 2005| Pages o1023-o1025

https://doi.org/10.1107/S160053680500752X

Redetermination of guaninium chloride dihydrate

Thomas C. Lewis ^a and Derek A. Tocher ^a ^*

^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), 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) were originally reported in 1951 (Broomhead, 1951 ), with a room-temperature X-ray determination performed 12 years later (Iball & Wilson, 1963 , 1965 ). 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.

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). 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). The two H atoms on the NH₂ group form two very dissimilar hydrogen bonds. A strong bond [N5—H7⋯N2^iv = 3.0162 (17) Å; see Table 1] is formed by one, while the second [N5—H6⋯Cl1ⁱ = 3.4368 (15) Å; see Table 1] 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
View of (I

), showing the atom labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Figure 2
The hydrogen-bonded (dashed lines) planar unit in (I

), showing the centrosymmetric dimer linked to four water molecules and two Cl⁻ ions. The other hydrogen bonds have been omitted for clarity.

Figure 3
The crystal packing of (I

), showing the complex three-dimensional hydrogen-bonding network (dashed lines).

Experimental

As part of an experimental polymorph screen on guanine, (I) 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
M_r = 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
D_x = 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 ) T_min = 0.850, T_max = 0.969
7902 measured reflections
2230 independent reflections
1891 reflections with I > 2σ(I)
R_int = 0.024
θ_max = 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(F_o²) + (0.0433P)² + 0.2271P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max = 0.001
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Table 1
Hydrogen-bonding geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯N2^iv	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⋯Cl1^v	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 ); 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 et al., 2002 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S160053680500752X/rn6044sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053680500752X/rn6044Isup2.hkl

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⁻·2H₂O	F(000) = 464
M_r = 223.63	D_x = 1.585 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 4.8587 (11) Å	Cell parameters from 2645 reflections
b = 13.228 (3) Å	θ = 2.1–28.2°
c = 14.612 (3) Å	µ = 0.40 mm⁻¹
β = 93.862 (4)°	T = 150 K
V = 937.0 (4) Å³	Block, colourless
Z = 4	0.42 × 0.12 × 0.08 mm

Data collection top

Bruker SMART APEX diffractometer	2230 independent reflections
Radiation source: fine-focus sealed tube	1891 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.024
ω rotation scans with narrow frames	θ_max = 28.2°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −6→6
T_min = 0.850, T_max = 0.969	k = −17→17
7902 measured reflections	l = −19→19

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.032	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.082	All H-atom parameters refined
S = 1.04	w = 1/[σ²(F_o²) + (0.0433P)² + 0.2271P] where P = (F_o² + 2F_c²)/3
2230 reflections	(Δ/σ)_max = 0.001
167 parameters	Δρ_max = 0.34 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

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

	x	y	z	U_iso*/U_eq
Cl1	1.11784 (8)	0.97938 (3)	0.33430 (2)	0.02731 (12)
O4	0.3146 (2)	0.70459 (7)	0.30721 (7)	0.0229 (2)
O1W	0.6924 (2)	0.83072 (9)	0.23556 (7)	0.0255 (2)
O2W	0.7162 (2)	0.90818 (9)	0.48276 (9)	0.0284 (3)
N1	−0.0342 (2)	0.60277 (9)	0.34807 (8)	0.0180 (2)
N2	−0.2267 (2)	0.59985 (8)	0.49343 (7)	0.0180 (2)
N3	−0.0027 (2)	0.72248 (9)	0.59658 (8)	0.0196 (3)
N4	0.2943 (2)	0.78712 (9)	0.50781 (8)	0.0192 (2)
N5	−0.3795 (3)	0.49067 (9)	0.37818 (9)	0.0214 (3)
C1	−0.2146 (3)	0.56538 (10)	0.40844 (9)	0.0170 (3)
C2	−0.0421 (3)	0.67400 (10)	0.51360 (9)	0.0171 (3)
C3	0.1454 (3)	0.71508 (10)	0.45727 (9)	0.0172 (3)
C4	0.1597 (3)	0.67858 (10)	0.36631 (9)	0.0177 (3)
C5	0.2011 (3)	0.78988 (11)	0.59023 (9)	0.0209 (3)
H1	−0.036 (4)	0.5739 (13)	0.2936 (13)	0.032 (5)*
H3	−0.095 (4)	0.7137 (14)	0.6449 (15)	0.041 (5)*
H4	0.429 (4)	0.8279 (14)	0.4882 (13)	0.037 (5)*
H5	0.268 (3)	0.8347 (13)	0.6416 (12)	0.025 (4)*
H6	−0.373 (3)	0.4697 (13)	0.3226 (13)	0.024 (4)*
H7	−0.500 (4)	0.4649 (13)	0.4145 (12)	0.030 (5)*
H3W	0.798 (4)	0.9297 (15)	0.4400 (14)	0.040 (6)*
H4W	0.747 (4)	0.9454 (16)	0.5301 (16)	0.044 (6)*
H1W	0.795 (4)	0.8675 (16)	0.2709 (13)	0.038 (5)*
H2W	0.585 (5)	0.7996 (17)	0.2697 (16)	0.053 (6)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0360 (2)	0.0291 (2)	0.01704 (18)	−0.00440 (15)	0.00350 (14)	0.00212 (13)
O4	0.0246 (5)	0.0255 (5)	0.0198 (5)	−0.0048 (4)	0.0099 (4)	−0.0002 (4)
O1W	0.0278 (6)	0.0296 (6)	0.0200 (5)	−0.0062 (5)	0.0088 (4)	−0.0019 (4)
O2W	0.0274 (6)	0.0339 (6)	0.0244 (6)	−0.0098 (5)	0.0061 (4)	−0.0052 (5)
N1	0.0195 (6)	0.0197 (6)	0.0154 (6)	−0.0012 (4)	0.0049 (4)	−0.0013 (4)
N2	0.0189 (5)	0.0184 (6)	0.0173 (6)	0.0006 (4)	0.0056 (4)	0.0006 (4)
N3	0.0228 (6)	0.0210 (6)	0.0156 (6)	0.0011 (5)	0.0056 (5)	−0.0007 (4)
N4	0.0190 (6)	0.0197 (6)	0.0193 (6)	−0.0010 (5)	0.0034 (4)	−0.0012 (4)
N5	0.0225 (6)	0.0226 (6)	0.0198 (6)	−0.0049 (5)	0.0069 (5)	−0.0022 (5)
C1	0.0165 (6)	0.0165 (6)	0.0183 (6)	0.0026 (5)	0.0039 (5)	0.0024 (5)
C2	0.0180 (6)	0.0172 (6)	0.0164 (6)	0.0035 (5)	0.0042 (5)	0.0009 (5)
C3	0.0166 (6)	0.0171 (6)	0.0182 (6)	0.0006 (5)	0.0032 (5)	0.0007 (5)
C4	0.0181 (6)	0.0176 (6)	0.0177 (6)	0.0019 (5)	0.0042 (5)	0.0019 (5)
C5	0.0226 (7)	0.0209 (7)	0.0194 (7)	0.0025 (5)	0.0020 (5)	−0.0017 (5)

Geometric parameters (Å, º) top

O4—C4	1.2321 (16)	N3—C2	1.3736 (18)
O1W—H1W	0.85 (2)	N3—H3	0.87 (2)
O1W—H2W	0.85 (2)	N4—C5	1.3154 (18)
O2W—H3W	0.81 (2)	N4—C3	1.3802 (18)
O2W—H4W	0.85 (2)	N4—H4	0.908 (19)
N1—C1	1.3769 (17)	N5—C1	1.3291 (18)
N1—C4	1.3892 (18)	N5—H6	0.861 (18)
N1—H1	0.883 (18)	N5—H7	0.886 (19)
N2—C1	1.3278 (18)	C2—C3	1.3797 (18)
N2—C2	1.3481 (17)	C3—C4	1.4202 (19)
N3—C5	1.3405 (19)	C5—H5	0.995 (17)

H1W—O1W—H2W	106.1 (19)	N2—C1—N5	120.19 (12)
H3W—O2W—H4W	110.7 (19)	N2—C1—N1	123.09 (12)
C1—N1—C4	126.10 (12)	N5—C1—N1	116.72 (12)
C1—N1—H1	117.0 (12)	N2—C2—N3	125.72 (12)
C4—N1—H1	116.8 (12)	N2—C2—C3	127.75 (12)
C1—N2—C2	112.57 (11)	N3—C2—C3	106.52 (12)
C5—N3—C2	108.01 (12)	C2—C3—N4	107.22 (12)
C5—N3—H3	124.6 (13)	C2—C3—C4	120.02 (12)
C2—N3—H3	127.4 (13)	N4—C3—C4	132.73 (12)
C5—N4—C3	107.99 (12)	O4—C4—N1	120.35 (12)
C5—N4—H4	124.9 (12)	O4—C4—C3	129.18 (13)
C3—N4—H4	127.1 (12)	N1—C4—C3	110.47 (11)
C1—N5—H6	119.5 (11)	N4—C5—N3	110.26 (12)
C1—N5—H7	119.8 (11)	N4—C5—H5	126.3 (10)
H6—N5—H7	120.6 (16)	N3—C5—H5	123.5 (9)

C2—N2—C1—N5	178.71 (12)	N3—C2—C3—C4	178.63 (11)
C2—N2—C1—N1	−0.62 (18)	C5—N4—C3—C2	−0.28 (15)
C4—N1—C1—N2	1.1 (2)	C5—N4—C3—C4	−178.36 (14)
C4—N1—C1—N5	−178.29 (12)	C1—N1—C4—O4	178.54 (12)
C1—N2—C2—N3	−178.52 (12)	C1—N1—C4—C3	−0.98 (18)
C1—N2—C2—C3	0.35 (19)	C2—C3—C4—O4	−178.82 (13)
C5—N3—C2—N2	178.93 (13)	N4—C3—C4—O4	−0.9 (3)
C5—N3—C2—C3	−0.14 (15)	C2—C3—C4—N1	0.65 (17)
N2—C2—C3—N4	−178.79 (13)	N4—C3—C4—N1	178.53 (14)
N3—C2—C3—N4	0.25 (14)	C3—N4—C5—N3	0.19 (16)
N2—C2—C3—C4	−0.4 (2)	C2—N3—C5—N4	−0.03 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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···N2^iv	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···Cl1^v	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) −x+1, y−1/2, −z+1/2; (ii) x−1, −y+3/2, z+1/2; (iii) −x, y−1/2, −z+1/2; (iv) −x−1, −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

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

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Volume 61| Part 4| April 2005| Pages o1023-o1025

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Redetermination of guaninium chloride dihydrate

Comment

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds