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The structure of the title compound, C4H9N4O+·I-, consists of discrete N9,N7-dimethyl­hypoxanthinium cations and iodide anions which are connected through hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805029375/nc6045sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536805029375/nc6045Isup2.hkl
Contains datablock I

CCDC reference: 287663

Key indicators

  • Single-crystal X-ray study
  • T = 173 K
  • Mean [sigma](C-C) = 0.009 Å
  • R factor = 0.042
  • wR factor = 0.108
  • Data-to-parameter ratio = 15.6

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low .... 0.95 PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.96 PLAT230_ALERT_2_C Hirshfeld Test Diff for N2 - C3 .. 5.09 su PLAT342_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 9
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

Methylation of DNA nucleic acid bases is an important and not well understood process. This reaction is catalysed by the enzyme DNA methyl transferase, which requires the co-factor S-adenosylmethionin. The methylated DNA-bases exert structural and functional effects on the DNA. For instance, the 5-methylcytosine favours the formation of left-handed DNA double helices (Z-DNA). In addition, N6-methyladenine exists in two rotameric states with only one of these forms able to establish base pairing. Methylation of DNA is used by bacteria to distinguish between their own and foreign DNA. Methylation starts immediately after replication. Each new strand is methylated; non-methylated DNA is recognized and digested by restriction enzymes. In natural DNA, the following methylated bases were discovered: 5-methylcytosine, N6-methyladenine, N4-methylcytosine and 5-hydroxymethyluracil (Bloomfield et al., 2000). The methylation of O6-methylguanine with methyliodide in dimethylformamide gives a mixture of O6,N3-dimethylguanine, N3-methylguanine and N3,N7dimethylguanine in a ratio of 1:1.3:1.3 (Kohda et al., 1987). With O6-methylhypoxanthine as the starting material, we obtained the title product, (I).

A perspective view of the title compound is shown in Fig. 1. The structure is composed of discrete N9,N7-dimethylhypoxanthinium cations and I anions. Bond lengths and angles can be regarded as normal (Cambridge Structural Database, Version 1.6 plus three updates; Mogul Version 1.0; Allen, 2002). Just the bond between N2 and C1 is rather long (Table 1). The crystal structure shows N—H···I hydrogen bonds and C—H···N, C—H···O and C—H···I contacts (Table 2).

Experimental top

O6-Methylhypoxanthine (0.5 g, 3.3 mmol) and methyl iodide (0.4 ml, 6.6 mmol, 2 equivalents) were refluxed in dimethylformamide (DMF, 100 ml) overnight. After removal of DMF under vacuum, single crystals of (I) were obtained.

Refinement top

All H atoms were located in a difference electron-density map, but were positioned with idealized geometry and refined with fixed individual displacement parameters [Uiso(H) = 1.2Ueq(C,N) or 1.5Ueq(methyl C)] using a riding model with N—H = 0.88 Å, and C—H = 0.95 and 0.98 Å for aromatic and methyl H atoms, respectively. The methyl groups were allowed to rotate but not to tip.

Computing details top

Data collection: X-AREA (Stoe & Cie, 2001); cell refinement: X-AREA; data reduction: X-AREA; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP in SHELXTL-Plus (Sheldrick, 1991); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003).

Figures top
[Figure 1] Fig. 1. Perspective view of the title compound, showing the atom numbering, with displacement ellipsoids drawn at the 50% probability level.
N9,N7-Dimethylhypoxanthinium iodide top
Crystal data top
C7H9N4O+·IF(000) = 560
Mr = 292.08Dx = 1.847 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 10175 reflections
a = 7.5961 (13) Åθ = 3.5–25.7°
b = 11.6988 (12) ŵ = 3.02 mm1
c = 11.8222 (15) ÅT = 173 K
β = 90.063 (12)°Plate, light red
V = 1050.6 (2) Å30.25 × 0.19 × 0.03 mm
Z = 4
Data collection top
Stoe IPDS-II two-circle
diffractometer
1866 independent reflections
Radiation source: fine-focus sealed tube1496 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.047
ω scansθmax = 25.6°, θmin = 3.6°
Absorption correction: multi-scan
(MULABS; Spek, 2003; Blessing, 1995)
h = 98
Tmin = 0.519, Tmax = 0.915k = 1414
6468 measured reflectionsl = 1414
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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.108H-atom parameters constrained
S = 1.02 w = 1/[σ2(Fo2) + (0.0735P)2]
where P = (Fo2 + 2Fc2)/3
1866 reflections(Δ/σ)max = 0.001
120 parametersΔρmax = 1.41 e Å3
0 restraintsΔρmin = 1.45 e Å3
Crystal data top
C7H9N4O+·IV = 1050.6 (2) Å3
Mr = 292.08Z = 4
Monoclinic, P21/nMo Kα radiation
a = 7.5961 (13) ŵ = 3.02 mm1
b = 11.6988 (12) ÅT = 173 K
c = 11.8222 (15) Å0.25 × 0.19 × 0.03 mm
β = 90.063 (12)°
Data collection top
Stoe IPDS-II two-circle
diffractometer
1866 independent reflections
Absorption correction: multi-scan
(MULABS; Spek, 2003; Blessing, 1995)
1496 reflections with I > 2σ(I)
Tmin = 0.519, Tmax = 0.915Rint = 0.047
6468 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.108H-atom parameters constrained
S = 1.02Δρmax = 1.41 e Å3
1866 reflectionsΔρmin = 1.45 e Å3
120 parameters
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
I10.63483 (6)0.82380 (3)0.61953 (3)0.03638 (18)
O10.3918 (8)0.4809 (5)0.7249 (5)0.0672 (16)
C10.5150 (11)0.4478 (6)0.6684 (6)0.0441 (16)
N20.6404 (9)0.5245 (6)0.6153 (5)0.0517 (15)
H20.61940.59830.62050.062*
C30.7847 (10)0.4929 (5)0.5592 (6)0.0431 (16)
H30.85780.55210.53060.052*
N40.8346 (9)0.3877 (5)0.5400 (5)0.0433 (13)
C50.7193 (9)0.3111 (5)0.5848 (5)0.0351 (14)
C60.5646 (9)0.3353 (5)0.6444 (5)0.0331 (13)
N70.4927 (7)0.2313 (4)0.6763 (4)0.0328 (11)
C70.3251 (12)0.2120 (7)0.7341 (7)0.060 (2)
H7A0.27250.14060.70690.091*
H7B0.24510.27580.71820.091*
H7C0.34550.20680.81580.091*
C80.5997 (10)0.1479 (5)0.6369 (5)0.0328 (14)
H80.58040.06830.64620.039*
N90.7358 (8)0.1941 (4)0.5833 (4)0.0316 (11)
C90.8788 (12)0.1282 (7)0.5296 (6)0.0520 (19)
H9A0.90640.06130.57620.078*
H9B0.98360.17650.52280.078*
H9C0.84120.10320.45430.078*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.0493 (3)0.0236 (2)0.0363 (2)0.00380 (18)0.01123 (16)0.00207 (15)
O10.060 (4)0.057 (3)0.085 (4)0.011 (3)0.020 (3)0.008 (3)
C10.053 (4)0.037 (4)0.042 (3)0.005 (3)0.006 (3)0.002 (3)
N20.063 (4)0.030 (3)0.062 (3)0.009 (3)0.009 (3)0.008 (3)
C30.053 (4)0.028 (3)0.049 (3)0.004 (3)0.003 (3)0.002 (3)
N40.054 (4)0.031 (3)0.046 (3)0.002 (3)0.002 (3)0.003 (2)
C50.044 (4)0.027 (3)0.034 (3)0.003 (3)0.008 (3)0.005 (2)
C60.045 (4)0.021 (3)0.033 (3)0.002 (3)0.006 (3)0.000 (2)
N70.043 (3)0.025 (2)0.031 (2)0.008 (2)0.004 (2)0.0011 (19)
C70.064 (6)0.055 (5)0.062 (5)0.013 (4)0.021 (4)0.001 (4)
C80.049 (4)0.020 (3)0.029 (3)0.007 (3)0.006 (3)0.000 (2)
N90.043 (3)0.017 (2)0.035 (2)0.000 (2)0.001 (2)0.0007 (18)
C90.063 (5)0.039 (4)0.053 (4)0.010 (4)0.011 (4)0.002 (3)
Geometric parameters (Å, º) top
O1—C11.214 (8)N7—C81.353 (9)
C1—C61.398 (9)N7—C71.463 (9)
C1—N21.453 (9)C7—H7A0.9800
N2—C31.334 (9)C7—H7B0.9800
N2—H20.8800C7—H7C0.9800
C3—N41.308 (8)C8—N91.328 (9)
C3—H30.9500C8—H80.9500
N4—C51.360 (8)N9—C91.475 (9)
C5—N91.375 (7)C9—H9A0.9800
C5—C61.399 (10)C9—H9B0.9800
C6—N71.386 (7)C9—H9C0.9800
O1—C1—C6128.4 (7)N7—C7—H7A109.5
O1—C1—N2123.1 (7)N7—C7—H7B109.5
C6—C1—N2108.5 (6)H7A—C7—H7B109.5
C3—N2—C1125.6 (6)N7—C7—H7C109.5
C3—N2—H2117.2H7A—C7—H7C109.5
C1—N2—H2117.2H7B—C7—H7C109.5
N4—C3—N2125.8 (6)N9—C8—N7109.9 (5)
N4—C3—H3117.1N9—C8—H8125.1
N2—C3—H3117.1N7—C8—H8125.1
C3—N4—C5111.5 (6)C8—N9—C5109.1 (5)
N4—C5—N9126.3 (6)C8—N9—C9124.5 (5)
N4—C5—C6127.1 (5)C5—N9—C9126.4 (6)
N9—C5—C6106.6 (5)N9—C9—H9A109.5
N7—C6—C1131.6 (6)N9—C9—H9B109.5
N7—C6—C5106.9 (5)H9A—C9—H9B109.5
C1—C6—C5121.3 (6)N9—C9—H9C109.5
C8—N7—C6107.5 (5)H9A—C9—H9C109.5
C8—N7—C7125.0 (6)H9B—C9—H9C109.5
C6—N7—C7127.3 (6)
O1—C1—N2—C3174.9 (8)N9—C5—C6—C1175.5 (6)
C6—C1—N2—C33.9 (10)C1—C6—N7—C8175.4 (8)
C1—N2—C3—N42.0 (12)C5—C6—N7—C80.3 (7)
N2—C3—N4—C50.1 (10)C1—C6—N7—C79.0 (12)
C3—N4—C5—N9177.6 (7)C5—C6—N7—C7175.8 (7)
C3—N4—C5—C60.2 (10)C6—N7—C8—N90.7 (7)
O1—C1—C6—N70.2 (14)C7—N7—C8—N9176.4 (7)
N2—C1—C6—N7178.5 (7)N7—C8—N9—C50.9 (7)
O1—C1—C6—C5174.8 (8)N7—C8—N9—C9180.0 (6)
N2—C1—C6—C54.0 (9)N4—C5—N9—C8178.8 (7)
N4—C5—C6—N7178.4 (6)C6—C5—N9—C80.7 (7)
N9—C5—C6—N70.3 (7)N4—C5—N9—C92.1 (11)
N4—C5—C6—C12.6 (11)C6—C5—N9—C9179.8 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···I10.882.643.502 (7)166
C3—H3···N4i0.952.583.420 (9)148
C7—H7A···O1ii0.982.393.203 (10)140
C8—H8···I1iii0.952.913.807 (6)159
Symmetry codes: (i) x+2, y+1, z+1; (ii) x+1/2, y1/2, z+3/2; (iii) x, y1, z.

Experimental details

Crystal data
Chemical formulaC7H9N4O+·I
Mr292.08
Crystal system, space groupMonoclinic, P21/n
Temperature (K)173
a, b, c (Å)7.5961 (13), 11.6988 (12), 11.8222 (15)
β (°) 90.063 (12)
V3)1050.6 (2)
Z4
Radiation typeMo Kα
µ (mm1)3.02
Crystal size (mm)0.25 × 0.19 × 0.03
Data collection
DiffractometerStoe IPDS-II two-circle
diffractometer
Absorption correctionMulti-scan
(MULABS; Spek, 2003; Blessing, 1995)
Tmin, Tmax0.519, 0.915
No. of measured, independent and
observed [I > 2σ(I)] reflections
6468, 1866, 1496
Rint0.047
(sin θ/λ)max1)0.607
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.108, 1.02
No. of reflections1866
No. of parameters120
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)1.41, 1.45

Computer programs: X-AREA (Stoe & Cie, 2001), X-AREA, SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), XP in SHELXTL-Plus (Sheldrick, 1991), SHELXL97 and PLATON (Spek, 2003).

Selected bond lengths (Å) top
O1—C11.214 (8)C5—C61.399 (10)
C1—N21.453 (9)C6—N71.386 (7)
N2—C31.334 (9)N7—C81.353 (9)
C3—N41.308 (8)N7—C71.463 (9)
N4—C51.360 (8)C8—N91.328 (9)
C5—N91.375 (7)N9—C91.475 (9)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2···I10.882.643.502 (7)166
C3—H3···N4i0.952.583.420 (9)148
C7—H7A···O1ii0.982.393.203 (10)140
C8—H8···I1iii0.952.913.807 (6)159
Symmetry codes: (i) x+2, y+1, z+1; (ii) x+1/2, y1/2, z+3/2; (iii) x, y1, z.
 

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