1-(4-Iodo­butyl)pyrimidin-1-ium iodide

Walji, D.V.B.; Storey, J.M.D.; Harrison, W.T.A.

doi:10.1107/S1600536807005028

organic compounds

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ISSN: 2056-9890

Volume 63| Part 3| March 2007| Pages o1222-o1223

https://doi.org/10.1107/S1600536807005028

1-(4-Iodobutyl)pyrimidin-1-ium iodide

Dhiran V. B. Walji,^a John M. D. Storey ^a and William T. A. Harrison ^a ^*

^aDepartment of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland
^*Correspondence e-mail: w.harrison@abdn.ac.uk

(Received 30 January 2007; accepted 30 January 2007; online 7 February 2007)

The title molecular salt, C₈H₁₂IN₂⁺·I⁻, features weak C—H⋯N and C—H⋯I interactions in the crystal structure.

Comment

As part of our investigations of substituted pyrimidines (Brown, 1994 ), the title compound, (I), C₈H₁₂IN₂⁺·I⁻, has been synthesized and structurally characterized (Fig. 1). Compound (I) possesses normal geometrical parameters (Allen et al., 1987 ). The pyrimidine ring (C5–C8/N1/N2; centroid Cg) is almost planar (r.m.s. deviation from the mean plane = 0.007 Å). The bond-angle sum at N1 of 360.0° implies the expected sp²-hybridization. The dihedral angle between the aromatic ring and the mean plane of the side-chain atoms (C1–C4/I1) is 53.63 (11)°.

A PLATON (Spek, 2003 ) analysis of (I) identified some short C—H⋯N and C—H⋯I interactions (Table 1) that might influence the crystal packing. Conversely, there are no π–π stacking interactions in (I), the shortest Cg⋯Cg separation being greater than 5.2 Å. The shortest I1⋯I2 contact of 3.7418 (3) Å in (I) is significantly less than the Bondi (1964 ) van der Waals I⋯I contact distance of 3.96 Å.

Figure 1
View of the molecular structure of (I)

showing the atom labelling and 50% probability displacement ellipsoids.

Experimental

Pyrimidine (2.50 mmol, 0.200 g) was carefully added to dry acetonitrile (60 ml) with stirring under nitrogen. The flask was degassed to remove any air and was stirred for 10 min. 1,4-Diiodobutane (10.1 mmol, 3.15 g) was then slowly added to the solution and the mixture was refluxed at 363 K for 8 h, monitoring the product using thin-layer chromatography (1:1 v/v, methanol, ethyl acetate, R_f = 0.5). The reaction vessel was covered with aluminium foil, as 1,4-diiodobutane is light-sensitive.

To ensure the complete consumption of pyrimidine, the reaction was stirred for a further 48 h. After this time, the reaction mixture was cooled to room temperature, revealing an orange crystalline product. The crystals were filtered off, washed with cold ethyl acetate (2 × 5 ml) and placed under reduced pressure to dry, yielding (I). The crystal quality was poor and not suitable for X-ray data collection.

The remaining filtrate was reduced in vacuo and washed with ethyl acetate (3 × 10 ml) to remove the excess 1,4-diiodobutane, producing an orange solid. This was dissolved in hot acetonitrile (20 ml), and recrystallization, initialized by a few drops of cold ethyl acetate, yielded orange rosettes in intergrown plates crystals of (I). The overall yield of both batches was 0.534 g (52%), m.p. 410–412 K. ν_max (KBr, cm⁻¹) 678 (alkyl-I), 817 (isolated aryl-H), 1431 (CH₂), 1619 (C=N, conjugated, cyclic), 2920 (CH₂), 3048 (CH-halogen).

Crystal data

C₈H₁₂IN₂⁺·I⁻
M_r = 390.00
Monoclinic, P 2₁ /c
a = 16.9178 (6) Å
b = 9.1694 (3) Å
c = 7.6303 (2) Å
β = 97.329 (2)°
V = 1173.99 (6) Å³
Z = 4
D_x = 2.207 Mg m⁻³
Mo Kα radiation
μ = 5.32 mm⁻¹
T = 120 (2) K
Plate, orange
0.22 × 0.18 × 0.02 mm

Data collection

Nonius KappaCCD diffractometer
ω and φ scans
Absorption correction: multi-scan (SADABS; Sheldrick, 2001 ) T_min = 0.388, T_max = 0.900
12760 measured reflections
2674 independent reflections
2302 reflections with I > 2σ(I)
R_int = 0.037
θ_max = 27.5°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.023
wR(F²) = 0.043
S = 1.09
2674 reflections
110 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.0082P)² + 0.8187P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max = 0.001
Δρ_max = 0.78 e Å⁻³
Δρ_min = −0.66 e Å⁻³
Extinction correction: SHELXL97
Extinction coefficient: 0.00174 (11)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C6—H6⋯N2ⁱ	0.95	2.58	3.396 (4)	144
C7—H7⋯I2ⁱⁱ	0.95	3.03	3.952 (3)	164
C8—H8⋯I2ⁱⁱⁱ	0.95	3.04	3.792 (3)	138
Symmetry codes: (i) $[-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) x+1, y, z; (iii) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

All H atoms were placed in calculated positions with C—H = 0.95–0.99 Å and refined as riding with U_iso(H) = 1.2U_eq(C).

Data collection: COLLECT (Nonius, 1998 ); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 ); data reduction: SCALEPACK and DENZO (Otwinowski & Minor, 1997), and SORTAV (Blessing, 1995 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536807005028/tk2131sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807005028/tk2131Isup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: SCALEPACK and DENZO (Otwinowski & Minor, 1997), and SORTAV (Blessing, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

1-(4-Iodobutyl)pyrimidin-1-ium iodide top

Crystal data top

C₈H₁₂IN₂⁺·I⁻	F(000) = 720
M_r = 390.00	D_x = 2.207 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2769 reflections
a = 16.9178 (6) Å	θ = 2.9–27.5°
b = 9.1694 (3) Å	µ = 5.32 mm⁻¹
c = 7.6303 (2) Å	T = 120 K
β = 97.329 (2)°	Slab, orange
V = 1173.99 (6) Å³	0.22 × 0.18 × 0.02 mm
Z = 4

Data collection top

Nonius KappaCCD diffractometer	2674 independent reflections
Radiation source: fine-focus sealed tube	2302 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.037
ω and φ scans	θ_max = 27.5°, θ_min = 3.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 2001)	h = −21→21
T_min = 0.388, T_max = 0.900	k = −11→11
12760 measured reflections	l = −8→9

Refinement top

Refinement on F²	Secondary atom site location: none
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.023	H-atom parameters constrained
wR(F²) = 0.043	w = 1/[σ²(F_o²) + (0.0082P)² + 0.8187P] where P = (F_o² + 2F_c²)/3
S = 1.09	(Δ/σ)_max = 0.001
2674 reflections	Δρ_max = 0.78 e Å⁻³
110 parameters	Δρ_min = −0.66 e Å⁻³
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.00174 (11)

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
C1	0.54275 (18)	0.3242 (3)	0.3053 (4)	0.0204 (7)
H1A	0.5677	0.3096	0.4286	0.024*
H1B	0.5456	0.2306	0.2417	0.024*
C2	0.58877 (17)	0.4387 (3)	0.2187 (4)	0.0178 (7)
H2A	0.5825	0.5343	0.2757	0.021*
H2B	0.5671	0.4473	0.0924	0.021*
C3	0.67736 (18)	0.3991 (3)	0.2346 (4)	0.0210 (7)
H3A	0.6976	0.3793	0.3599	0.025*
H3B	0.6842	0.3095	0.1658	0.025*
C4	0.72465 (19)	0.5222 (3)	0.1668 (4)	0.0225 (7)
H4A	0.7074	0.5356	0.0389	0.027*
H4B	0.7133	0.6137	0.2277	0.027*
C5	0.8421 (2)	0.3727 (3)	0.1321 (4)	0.0255 (7)
H5	0.8081	0.3034	0.0680	0.031*
C6	0.9232 (2)	0.3494 (4)	0.1607 (4)	0.0298 (8)
H6	0.9461	0.2632	0.1200	0.036*
C7	0.9699 (2)	0.4549 (4)	0.2501 (4)	0.0314 (8)
H7	1.0260	0.4405	0.2699	0.038*
C8	0.8615 (2)	0.5916 (3)	0.2825 (4)	0.0262 (7)
H8	0.8388	0.6766	0.3266	0.031*
N1	0.81170 (15)	0.4937 (3)	0.1953 (3)	0.0188 (6)
N2	0.93938 (17)	0.5776 (3)	0.3106 (4)	0.0344 (7)
I1	0.419543 (11)	0.38361 (2)	0.30573 (2)	0.01817 (7)
I2	0.204826 (12)	0.48311 (2)	0.30184 (3)	0.02537 (8)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0175 (17)	0.0191 (16)	0.0256 (16)	0.0038 (13)	0.0066 (13)	0.0007 (13)
C2	0.0153 (17)	0.0203 (16)	0.0177 (15)	0.0008 (12)	0.0016 (12)	0.0009 (12)
C3	0.0161 (18)	0.0191 (16)	0.0278 (17)	0.0011 (13)	0.0031 (13)	0.0014 (13)
C4	0.0132 (18)	0.0243 (17)	0.0302 (18)	0.0038 (13)	0.0035 (13)	0.0038 (14)
C5	0.0209 (19)	0.0222 (18)	0.0338 (19)	0.0023 (14)	0.0047 (14)	0.0002 (14)
C6	0.021 (2)	0.0267 (18)	0.042 (2)	0.0095 (15)	0.0071 (16)	0.0021 (16)
C7	0.0135 (19)	0.041 (2)	0.040 (2)	−0.0024 (16)	0.0027 (15)	0.0084 (17)
C8	0.023 (2)	0.0217 (17)	0.0341 (19)	−0.0017 (14)	0.0035 (15)	0.0007 (14)
N1	0.0136 (15)	0.0193 (14)	0.0233 (14)	0.0009 (11)	0.0013 (11)	0.0041 (11)
N2	0.0206 (17)	0.0363 (18)	0.0458 (19)	−0.0064 (14)	0.0032 (14)	−0.0017 (14)
I1	0.01703 (13)	0.01706 (12)	0.02101 (12)	−0.00227 (8)	0.00464 (8)	−0.00121 (8)
I2	0.01859 (14)	0.02792 (13)	0.03015 (13)	−0.00015 (9)	0.00529 (9)	−0.00106 (9)

Geometric parameters (Å, º) top

C1—C2	1.509 (4)	C4—H4B	0.9900
C1—I1	2.155 (3)	C5—N1	1.339 (4)
C1—H1A	0.9900	C5—C6	1.379 (4)
C1—H1B	0.9900	C5—H5	0.9500
C2—C3	1.532 (4)	C6—C7	1.374 (5)
C2—H2A	0.9900	C6—H6	0.9500
C2—H2B	0.9900	C7—N2	1.344 (4)
C3—C4	1.512 (4)	C7—H7	0.9500
C3—H3A	0.9900	C8—N2	1.313 (4)
C3—H3B	0.9900	C8—N1	1.348 (4)
C4—N1	1.484 (4)	C8—H8	0.9500
C4—H4A	0.9900

C2—C1—I1	112.19 (19)	C3—C4—H4A	109.2
C2—C1—H1A	109.2	N1—C4—H4B	109.2
I1—C1—H1A	109.2	C3—C4—H4B	109.2
C2—C1—H1B	109.2	H4A—C4—H4B	107.9
I1—C1—H1B	109.2	N1—C5—C6	119.5 (3)
H1A—C1—H1B	107.9	N1—C5—H5	120.3
C1—C2—C3	110.8 (2)	C6—C5—H5	120.3
C1—C2—H2A	109.5	C7—C6—C5	117.9 (3)
C3—C2—H2A	109.5	C7—C6—H6	121.1
C1—C2—H2B	109.5	C5—C6—H6	121.1
C3—C2—H2B	109.5	N2—C7—C6	122.5 (3)
H2A—C2—H2B	108.1	N2—C7—H7	118.7
C4—C3—C2	110.5 (2)	C6—C7—H7	118.7
C4—C3—H3A	109.5	N2—C8—N1	124.5 (3)
C2—C3—H3A	109.5	N2—C8—H8	117.7
C4—C3—H3B	109.5	N1—C8—H8	117.7
C2—C3—H3B	109.5	C5—N1—C8	119.0 (3)
H3A—C3—H3B	108.1	C5—N1—C4	120.8 (3)
N1—C4—C3	112.2 (2)	C8—N1—C4	120.1 (3)
N1—C4—H4A	109.2	C8—N2—C7	116.6 (3)

I1—C1—C2—C3	175.21 (19)	N2—C8—N1—C5	0.2 (5)
C1—C2—C3—C4	−173.5 (3)	N2—C8—N1—C4	−178.4 (3)
C2—C3—C4—N1	174.7 (2)	C3—C4—N1—C5	56.1 (4)
N1—C5—C6—C7	−1.7 (5)	C3—C4—N1—C8	−125.3 (3)
C5—C6—C7—N2	0.5 (5)	N1—C8—N2—C7	−1.4 (5)
C6—C5—N1—C8	1.4 (4)	C6—C7—N2—C8	1.0 (5)
C6—C5—N1—C4	180.0 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6···N2ⁱ	0.95	2.58	3.396 (4)	144
C7—H7···I2ⁱⁱ	0.95	3.03	3.952 (3)	164
C8—H8···I2ⁱⁱⁱ	0.95	3.04	3.792 (3)	138

Symmetry codes: (i) −x+2, y−1/2, −z+1/2; (ii) x+1, y, z; (iii) −x+1, y+1/2, −z+1/2.

Acknowledgements

We thank the EPSRC UK National Crystallography Service (University of Southampton) for the data collection.

References

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