Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805029375/nc6045sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536805029375/nc6045Isup2.hkl |
CCDC reference: 287663
Key indicators
- Single-crystal X-ray study
- T = 173 K
- Mean (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
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.
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.
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).
Fig. 1. Perspective view of the title compound, showing the atom numbering, with displacement ellipsoids drawn at the 50% probability level. |
C7H9N4O+·I− | F(000) = 560 |
Mr = 292.08 | Dx = 1.847 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 10175 reflections |
a = 7.5961 (13) Å | θ = 3.5–25.7° |
b = 11.6988 (12) Å | µ = 3.02 mm−1 |
c = 11.8222 (15) Å | T = 173 K |
β = 90.063 (12)° | Plate, light red |
V = 1050.6 (2) Å3 | 0.25 × 0.19 × 0.03 mm |
Z = 4 |
Stoe IPDS-II two-circle diffractometer | 1866 independent reflections |
Radiation source: fine-focus sealed tube | 1496 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.047 |
ω scans | θmax = 25.6°, θmin = 3.6° |
Absorption correction: multi-scan (MULABS; Spek, 2003; Blessing, 1995) | h = −9→8 |
Tmin = 0.519, Tmax = 0.915 | k = −14→14 |
6468 measured reflections | l = −14→14 |
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)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.108 | H-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 parameters | Δρmax = 1.41 e Å−3 |
0 restraints | Δρmin = −1.45 e Å−3 |
C7H9N4O+·I− | V = 1050.6 (2) Å3 |
Mr = 292.08 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 7.5961 (13) Å | µ = 3.02 mm−1 |
b = 11.6988 (12) Å | T = 173 K |
c = 11.8222 (15) Å | 0.25 × 0.19 × 0.03 mm |
β = 90.063 (12)° |
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 = 0.915 | Rint = 0.047 |
6468 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.108 | H-atom parameters constrained |
S = 1.02 | Δρmax = 1.41 e Å−3 |
1866 reflections | Δρmin = −1.45 e Å−3 |
120 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
I1 | 0.63483 (6) | 0.82380 (3) | 0.61953 (3) | 0.03638 (18) | |
O1 | 0.3918 (8) | 0.4809 (5) | 0.7249 (5) | 0.0672 (16) | |
C1 | 0.5150 (11) | 0.4478 (6) | 0.6684 (6) | 0.0441 (16) | |
N2 | 0.6404 (9) | 0.5245 (6) | 0.6153 (5) | 0.0517 (15) | |
H2 | 0.6194 | 0.5983 | 0.6205 | 0.062* | |
C3 | 0.7847 (10) | 0.4929 (5) | 0.5592 (6) | 0.0431 (16) | |
H3 | 0.8578 | 0.5521 | 0.5306 | 0.052* | |
N4 | 0.8346 (9) | 0.3877 (5) | 0.5400 (5) | 0.0433 (13) | |
C5 | 0.7193 (9) | 0.3111 (5) | 0.5848 (5) | 0.0351 (14) | |
C6 | 0.5646 (9) | 0.3353 (5) | 0.6444 (5) | 0.0331 (13) | |
N7 | 0.4927 (7) | 0.2313 (4) | 0.6763 (4) | 0.0328 (11) | |
C7 | 0.3251 (12) | 0.2120 (7) | 0.7341 (7) | 0.060 (2) | |
H7A | 0.2725 | 0.1406 | 0.7069 | 0.091* | |
H7B | 0.2451 | 0.2758 | 0.7182 | 0.091* | |
H7C | 0.3455 | 0.2068 | 0.8158 | 0.091* | |
C8 | 0.5997 (10) | 0.1479 (5) | 0.6369 (5) | 0.0328 (14) | |
H8 | 0.5804 | 0.0683 | 0.6462 | 0.039* | |
N9 | 0.7358 (8) | 0.1941 (4) | 0.5833 (4) | 0.0316 (11) | |
C9 | 0.8788 (12) | 0.1282 (7) | 0.5296 (6) | 0.0520 (19) | |
H9A | 0.9064 | 0.0613 | 0.5762 | 0.078* | |
H9B | 0.9836 | 0.1765 | 0.5228 | 0.078* | |
H9C | 0.8412 | 0.1032 | 0.4543 | 0.078* |
U11 | U22 | U33 | U12 | U13 | U23 | |
I1 | 0.0493 (3) | 0.0236 (2) | 0.0363 (2) | −0.00380 (18) | −0.01123 (16) | 0.00207 (15) |
O1 | 0.060 (4) | 0.057 (3) | 0.085 (4) | 0.011 (3) | 0.020 (3) | −0.008 (3) |
C1 | 0.053 (4) | 0.037 (4) | 0.042 (3) | 0.005 (3) | −0.006 (3) | −0.002 (3) |
N2 | 0.063 (4) | 0.030 (3) | 0.062 (3) | −0.009 (3) | −0.009 (3) | 0.008 (3) |
C3 | 0.053 (4) | 0.028 (3) | 0.049 (3) | −0.004 (3) | 0.003 (3) | 0.002 (3) |
N4 | 0.054 (4) | 0.031 (3) | 0.046 (3) | −0.002 (3) | 0.002 (3) | 0.003 (2) |
C5 | 0.044 (4) | 0.027 (3) | 0.034 (3) | 0.003 (3) | −0.008 (3) | −0.005 (2) |
C6 | 0.045 (4) | 0.021 (3) | 0.033 (3) | −0.002 (3) | −0.006 (3) | 0.000 (2) |
N7 | 0.043 (3) | 0.025 (2) | 0.031 (2) | −0.008 (2) | −0.004 (2) | 0.0011 (19) |
C7 | 0.064 (6) | 0.055 (5) | 0.062 (5) | −0.013 (4) | 0.021 (4) | −0.001 (4) |
C8 | 0.049 (4) | 0.020 (3) | 0.029 (3) | −0.007 (3) | −0.006 (3) | 0.000 (2) |
N9 | 0.043 (3) | 0.017 (2) | 0.035 (2) | 0.000 (2) | 0.001 (2) | −0.0007 (18) |
C9 | 0.063 (5) | 0.039 (4) | 0.053 (4) | 0.010 (4) | 0.011 (4) | −0.002 (3) |
O1—C1 | 1.214 (8) | N7—C8 | 1.353 (9) |
C1—C6 | 1.398 (9) | N7—C7 | 1.463 (9) |
C1—N2 | 1.453 (9) | C7—H7A | 0.9800 |
N2—C3 | 1.334 (9) | C7—H7B | 0.9800 |
N2—H2 | 0.8800 | C7—H7C | 0.9800 |
C3—N4 | 1.308 (8) | C8—N9 | 1.328 (9) |
C3—H3 | 0.9500 | C8—H8 | 0.9500 |
N4—C5 | 1.360 (8) | N9—C9 | 1.475 (9) |
C5—N9 | 1.375 (7) | C9—H9A | 0.9800 |
C5—C6 | 1.399 (10) | C9—H9B | 0.9800 |
C6—N7 | 1.386 (7) | C9—H9C | 0.9800 |
O1—C1—C6 | 128.4 (7) | N7—C7—H7A | 109.5 |
O1—C1—N2 | 123.1 (7) | N7—C7—H7B | 109.5 |
C6—C1—N2 | 108.5 (6) | H7A—C7—H7B | 109.5 |
C3—N2—C1 | 125.6 (6) | N7—C7—H7C | 109.5 |
C3—N2—H2 | 117.2 | H7A—C7—H7C | 109.5 |
C1—N2—H2 | 117.2 | H7B—C7—H7C | 109.5 |
N4—C3—N2 | 125.8 (6) | N9—C8—N7 | 109.9 (5) |
N4—C3—H3 | 117.1 | N9—C8—H8 | 125.1 |
N2—C3—H3 | 117.1 | N7—C8—H8 | 125.1 |
C3—N4—C5 | 111.5 (6) | C8—N9—C5 | 109.1 (5) |
N4—C5—N9 | 126.3 (6) | C8—N9—C9 | 124.5 (5) |
N4—C5—C6 | 127.1 (5) | C5—N9—C9 | 126.4 (6) |
N9—C5—C6 | 106.6 (5) | N9—C9—H9A | 109.5 |
N7—C6—C1 | 131.6 (6) | N9—C9—H9B | 109.5 |
N7—C6—C5 | 106.9 (5) | H9A—C9—H9B | 109.5 |
C1—C6—C5 | 121.3 (6) | N9—C9—H9C | 109.5 |
C8—N7—C6 | 107.5 (5) | H9A—C9—H9C | 109.5 |
C8—N7—C7 | 125.0 (6) | H9B—C9—H9C | 109.5 |
C6—N7—C7 | 127.3 (6) | ||
O1—C1—N2—C3 | 174.9 (8) | N9—C5—C6—C1 | 175.5 (6) |
C6—C1—N2—C3 | −3.9 (10) | C1—C6—N7—C8 | −175.4 (8) |
C1—N2—C3—N4 | 2.0 (12) | C5—C6—N7—C8 | −0.3 (7) |
N2—C3—N4—C5 | 0.1 (10) | C1—C6—N7—C7 | 9.0 (12) |
C3—N4—C5—N9 | −177.6 (7) | C5—C6—N7—C7 | −175.8 (7) |
C3—N4—C5—C6 | 0.2 (10) | C6—N7—C8—N9 | 0.7 (7) |
O1—C1—C6—N7 | −0.2 (14) | C7—N7—C8—N9 | 176.4 (7) |
N2—C1—C6—N7 | 178.5 (7) | N7—C8—N9—C5 | −0.9 (7) |
O1—C1—C6—C5 | −174.8 (8) | N7—C8—N9—C9 | 180.0 (6) |
N2—C1—C6—C5 | 4.0 (9) | N4—C5—N9—C8 | 178.8 (7) |
N4—C5—C6—N7 | −178.4 (6) | C6—C5—N9—C8 | 0.7 (7) |
N9—C5—C6—N7 | −0.3 (7) | N4—C5—N9—C9 | −2.1 (11) |
N4—C5—C6—C1 | −2.6 (11) | C6—C5—N9—C9 | 179.8 (7) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···I1 | 0.88 | 2.64 | 3.502 (7) | 166 |
C3—H3···N4i | 0.95 | 2.58 | 3.420 (9) | 148 |
C7—H7A···O1ii | 0.98 | 2.39 | 3.203 (10) | 140 |
C8—H8···I1iii | 0.95 | 2.91 | 3.807 (6) | 159 |
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1/2, y−1/2, −z+3/2; (iii) x, y−1, z. |
Experimental details
Crystal data | |
Chemical formula | C7H9N4O+·I− |
Mr | 292.08 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 173 |
a, b, c (Å) | 7.5961 (13), 11.6988 (12), 11.8222 (15) |
β (°) | 90.063 (12) |
V (Å3) | 1050.6 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 3.02 |
Crystal size (mm) | 0.25 × 0.19 × 0.03 |
Data collection | |
Diffractometer | Stoe IPDS-II two-circle diffractometer |
Absorption correction | Multi-scan (MULABS; Spek, 2003; Blessing, 1995) |
Tmin, Tmax | 0.519, 0.915 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6468, 1866, 1496 |
Rint | 0.047 |
(sin θ/λ)max (Å−1) | 0.607 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.108, 1.02 |
No. of reflections | 1866 |
No. of parameters | 120 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
O1—C1 | 1.214 (8) | C5—C6 | 1.399 (10) |
C1—N2 | 1.453 (9) | C6—N7 | 1.386 (7) |
N2—C3 | 1.334 (9) | N7—C8 | 1.353 (9) |
C3—N4 | 1.308 (8) | N7—C7 | 1.463 (9) |
N4—C5 | 1.360 (8) | C8—N9 | 1.328 (9) |
C5—N9 | 1.375 (7) | N9—C9 | 1.475 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···I1 | 0.88 | 2.64 | 3.502 (7) | 166 |
C3—H3···N4i | 0.95 | 2.58 | 3.420 (9) | 148 |
C7—H7A···O1ii | 0.98 | 2.39 | 3.203 (10) | 140 |
C8—H8···I1iii | 0.95 | 2.91 | 3.807 (6) | 159 |
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1/2, y−1/2, −z+3/2; (iii) x, y−1, z. |
Subscribe to Acta Crystallographica Section E: Crystallographic Communications
The full text of this article is available to subscribers to the journal.
- Information on subscribing
- Sample issue
- If you have already subscribed, you may need to register
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).