Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807046090/lh2511sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807046090/lh2511Isup2.hkl |
CCDC reference: 667324
Key indicators
- Single-crystal X-ray study
- T = 93 K
- Mean (C-C) = 0.003 Å
- R factor = 0.019
- wR factor = 0.047
- Data-to-parameter ratio = 16.5
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT062_ALERT_4_C Rescale T(min) & T(max) by ..................... 0.99 PLAT411_ALERT_2_C Short Inter H...H Contact H6A .. H6A .. 2.13 Ang.
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 2 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 0 ALERT type 3 Indicator that the structure quality may be low 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For background, see: Javet et al. (2007). For reference structural data, see: Allen et al. (1995).
4-Aminomethylpyridine was aceylated with acetic anhydride in water, followed by methylation with CH3I in CH2Cl2, yielding yellow cubic blocks of (I) after solvent removal.
The N-bound hydrogen atom was located in a difference map and its position was freely refined with Uiso(H) = 1.2Ueq(N). The C-bound hydrogen atoms were geometrically placed (C—H = 0.95–0.99 Å) and refined as riding with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C). The methyl groups were allowed to rotate, but not tip, to best fit the electron density.
The title compound, (I) (Fig. 1), is an intermediate in the synthesis of azacyanine dyes (Javet et al., 2007) The dihedral angle between the C1—C5/N1 pyrininium ring and the C7/C8/N2/O1 grouping in (I) is 73.93 (8)°. Otherwise, the geometry of (I) may be regarded as normal (Allen et al., 1995).
In the crystal of (I), an N—H···I hydrogen bond (Table 1) links the cation and the anion. A weak C—H···O interaction may also help to consolidate the packing, leading to [001] chains. There are no aromatic π-π stacking interactions in (I) as the closest centroid-centroid separation is greater than 4.37 Å.
For background, see: Javet et al. (2007). For reference structural data, see: Allen et al. (1995).
Data collection: CrystalClear (Rigaku, 2004); cell refinement: CrystalClear (Rigaku, 2004); data reduction: CrystalClear (Rigaku, 2004); 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 (Sheldrick, 1997).
Fig. 1. View of the molecular structure of (I) showing 50% displacement ellipsoids (arbitrary spheres for the H atoms). The hydrogen bond is indicated by a double-dashed line. |
C9H13N2O+·I− | Z = 4 |
Mr = 292.11 | F(000) = 568 |
Monoclinic, P21/c | Dx = 1.712 Mg m−3 |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 8.597 (2) Å | µ = 2.79 mm−1 |
b = 12.986 (3) Å | T = 93 K |
c = 10.335 (3) Å | Cube, yellow |
β = 100.802 (5)° | 0.10 × 0.10 × 0.10 mm |
V = 1133.4 (5) Å3 |
Rigaku Mercury CCD diffractometer | 1932 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.023 |
Graphite monochromator | θmax = 25.3°, θmin = 2.4° |
ω and φ scans | h = −9→10 |
6776 measured reflections | k = −15→14 |
2035 independent reflections | l = −11→12 |
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)] = 0.019 | Hydrogen site location: difmap and geom |
wR(F2) = 0.048 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0262P)2 + 0.8567P] where P = (Fo2 + 2Fc2)/3 |
2035 reflections | (Δ/σ)max = 0.002 |
123 parameters | Δρmax = 0.82 e Å−3 |
0 restraints | Δρmin = −0.46 e Å−3 |
C9H13N2O+·I− | V = 1133.4 (5) Å3 |
Mr = 292.11 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.597 (2) Å | µ = 2.79 mm−1 |
b = 12.986 (3) Å | T = 93 K |
c = 10.335 (3) Å | 0.10 × 0.10 × 0.10 mm |
β = 100.802 (5)° |
Rigaku Mercury CCD diffractometer | 1932 reflections with I > 2σ(I) |
6776 measured reflections | Rint = 0.023 |
2035 independent reflections |
R[F2 > 2σ(F2)] = 0.019 | 0 restraints |
wR(F2) = 0.048 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.82 e Å−3 |
2035 reflections | Δρmin = −0.46 e Å−3 |
123 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 | ||
C1 | 0.1654 (3) | 0.42190 (17) | 0.5581 (2) | 0.0205 (5) | |
H1 | 0.1710 | 0.3976 | 0.4724 | 0.025* | |
C2 | 0.0883 (3) | 0.36517 (17) | 0.6378 (2) | 0.0196 (4) | |
H2A | 0.0395 | 0.3020 | 0.6066 | 0.024* | |
C3 | 0.1502 (3) | 0.48747 (17) | 0.8068 (2) | 0.0207 (5) | |
H3 | 0.1445 | 0.5094 | 0.8935 | 0.025* | |
C4 | 0.2286 (3) | 0.54695 (17) | 0.7301 (2) | 0.0202 (5) | |
H4 | 0.2778 | 0.6093 | 0.7640 | 0.024* | |
C5 | 0.2361 (2) | 0.51580 (16) | 0.6022 (2) | 0.0176 (4) | |
C6 | 0.3140 (3) | 0.57832 (18) | 0.5096 (2) | 0.0226 (5) | |
H6A | 0.3852 | 0.5326 | 0.4708 | 0.027* | |
H6B | 0.2309 | 0.6033 | 0.4368 | 0.027* | |
C7 | 0.3626 (3) | 0.76363 (17) | 0.5334 (2) | 0.0200 (5) | |
C8 | 0.4766 (3) | 0.84538 (18) | 0.5954 (3) | 0.0278 (5) | |
H8A | 0.5497 | 0.8161 | 0.6705 | 0.042* | |
H8B | 0.4176 | 0.9023 | 0.6257 | 0.042* | |
H8C | 0.5366 | 0.8711 | 0.5303 | 0.042* | |
C9 | −0.0093 (3) | 0.33746 (18) | 0.8422 (2) | 0.0255 (5) | |
H9A | −0.0177 | 0.2660 | 0.8113 | 0.038* | |
H9B | −0.1156 | 0.3668 | 0.8352 | 0.038* | |
H9C | 0.0455 | 0.3394 | 0.9343 | 0.038* | |
N1 | 0.0809 (2) | 0.39812 (12) | 0.76054 (19) | 0.0179 (4) | |
N2 | 0.4043 (2) | 0.66579 (14) | 0.5685 (2) | 0.0218 (4) | |
H2 | 0.485 (3) | 0.655 (2) | 0.617 (3) | 0.026* | |
O1 | 0.23978 (19) | 0.78412 (13) | 0.45526 (17) | 0.0281 (4) | |
I1 | 0.753932 (15) | 0.602150 (10) | 0.806080 (13) | 0.01921 (7) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0250 (12) | 0.0206 (10) | 0.0147 (11) | 0.0018 (9) | 0.0008 (9) | −0.0032 (9) |
C2 | 0.0237 (11) | 0.0155 (10) | 0.0178 (11) | 0.0024 (9) | −0.0006 (9) | −0.0033 (9) |
C3 | 0.0208 (11) | 0.0238 (11) | 0.0155 (11) | 0.0028 (9) | −0.0016 (9) | −0.0045 (9) |
C4 | 0.0203 (11) | 0.0170 (10) | 0.0212 (11) | 0.0014 (8) | −0.0020 (9) | −0.0068 (9) |
C5 | 0.0149 (10) | 0.0173 (10) | 0.0183 (11) | 0.0051 (8) | −0.0031 (8) | 0.0005 (8) |
C6 | 0.0224 (12) | 0.0222 (10) | 0.0219 (12) | 0.0002 (9) | 0.0010 (10) | −0.0007 (9) |
C7 | 0.0195 (11) | 0.0221 (11) | 0.0196 (11) | 0.0011 (9) | 0.0070 (9) | 0.0024 (9) |
C8 | 0.0269 (12) | 0.0206 (11) | 0.0360 (14) | −0.0033 (9) | 0.0061 (11) | 0.0019 (10) |
C9 | 0.0291 (12) | 0.0270 (12) | 0.0194 (12) | −0.0006 (10) | 0.0020 (10) | 0.0044 (9) |
N1 | 0.0176 (10) | 0.0191 (9) | 0.0150 (10) | 0.0035 (7) | −0.0017 (8) | 0.0010 (7) |
N2 | 0.0178 (9) | 0.0202 (9) | 0.0243 (11) | 0.0003 (7) | −0.0039 (8) | 0.0027 (8) |
O1 | 0.0246 (9) | 0.0277 (9) | 0.0300 (10) | 0.0024 (7) | 0.0002 (7) | 0.0102 (7) |
I1 | 0.01935 (11) | 0.02071 (10) | 0.01594 (11) | −0.00113 (5) | −0.00091 (7) | 0.00050 (5) |
C1—C2 | 1.365 (3) | C6—H6B | 0.9900 |
C1—C5 | 1.400 (3) | C7—O1 | 1.232 (3) |
C1—H1 | 0.9500 | C7—N2 | 1.351 (3) |
C2—N1 | 1.352 (3) | C7—C8 | 1.504 (3) |
C2—H2A | 0.9500 | C8—H8A | 0.9800 |
C3—N1 | 1.350 (3) | C8—H8B | 0.9800 |
C3—C4 | 1.371 (3) | C8—H8C | 0.9800 |
C3—H3 | 0.9500 | C9—N1 | 1.476 (3) |
C4—C5 | 1.395 (3) | C9—H9A | 0.9800 |
C4—H4 | 0.9500 | C9—H9B | 0.9800 |
C5—C6 | 1.505 (3) | C9—H9C | 0.9800 |
C6—N2 | 1.445 (3) | N2—H2 | 0.79 (3) |
C6—H6A | 0.9900 | ||
C2—C1—C5 | 120.2 (2) | O1—C7—N2 | 122.1 (2) |
C2—C1—H1 | 119.9 | O1—C7—C8 | 122.4 (2) |
C5—C1—H1 | 119.9 | N2—C7—C8 | 115.5 (2) |
N1—C2—C1 | 120.6 (2) | C7—C8—H8A | 109.5 |
N1—C2—H2A | 119.7 | C7—C8—H8B | 109.5 |
C1—C2—H2A | 119.7 | H8A—C8—H8B | 109.5 |
N1—C3—C4 | 120.8 (2) | C7—C8—H8C | 109.5 |
N1—C3—H3 | 119.6 | H8A—C8—H8C | 109.5 |
C4—C3—H3 | 119.6 | H8B—C8—H8C | 109.5 |
C3—C4—C5 | 120.0 (2) | N1—C9—H9A | 109.5 |
C3—C4—H4 | 120.0 | N1—C9—H9B | 109.5 |
C5—C4—H4 | 120.0 | H9A—C9—H9B | 109.5 |
C4—C5—C1 | 117.8 (2) | N1—C9—H9C | 109.5 |
C4—C5—C6 | 123.5 (2) | H9A—C9—H9C | 109.5 |
C1—C5—C6 | 118.7 (2) | H9B—C9—H9C | 109.5 |
N2—C6—C5 | 115.13 (19) | C3—N1—C2 | 120.60 (19) |
N2—C6—H6A | 108.5 | C3—N1—C9 | 120.02 (19) |
C5—C6—H6A | 108.5 | C2—N1—C9 | 119.34 (18) |
N2—C6—H6B | 108.5 | C7—N2—C6 | 122.1 (2) |
C5—C6—H6B | 108.5 | C7—N2—H2 | 120 (2) |
H6A—C6—H6B | 107.5 | C6—N2—H2 | 118 (2) |
C5—C1—C2—N1 | −0.8 (3) | C4—C3—N1—C2 | 0.4 (3) |
N1—C3—C4—C5 | 0.7 (3) | C4—C3—N1—C9 | −177.2 (2) |
C3—C4—C5—C1 | −1.7 (3) | C1—C2—N1—C3 | −0.3 (3) |
C3—C4—C5—C6 | 177.5 (2) | C1—C2—N1—C9 | 177.3 (2) |
C2—C1—C5—C4 | 1.8 (3) | O1—C7—N2—C6 | 4.6 (3) |
C2—C1—C5—C6 | −177.4 (2) | C8—C7—N2—C6 | −174.9 (2) |
C4—C5—C6—N2 | 9.8 (3) | C5—C6—N2—C7 | −115.1 (2) |
C1—C5—C6—N2 | −171.05 (19) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···I1 | 0.79 (3) | 2.81 (3) | 3.603 (2) | 174 (3) |
C4—H4···O1i | 0.95 | 2.48 | 3.186 (3) | 131 |
Symmetry code: (i) x, −y+3/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C9H13N2O+·I− |
Mr | 292.11 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 93 |
a, b, c (Å) | 8.597 (2), 12.986 (3), 10.335 (3) |
β (°) | 100.802 (5) |
V (Å3) | 1133.4 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 2.79 |
Crystal size (mm) | 0.10 × 0.10 × 0.10 |
Data collection | |
Diffractometer | Rigaku Mercury CCD |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6776, 2035, 1932 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.602 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.019, 0.048, 1.04 |
No. of reflections | 2035 |
No. of parameters | 123 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.82, −0.46 |
Computer programs: CrystalClear (Rigaku, 2004), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···I1 | 0.79 (3) | 2.81 (3) | 3.603 (2) | 174 (3) |
C4—H4···O1i | 0.95 | 2.48 | 3.186 (3) | 131 |
Symmetry code: (i) x, −y+3/2, z+1/2. |
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The title compound, (I) (Fig. 1), is an intermediate in the synthesis of azacyanine dyes (Javet et al., 2007) The dihedral angle between the C1—C5/N1 pyrininium ring and the C7/C8/N2/O1 grouping in (I) is 73.93 (8)°. Otherwise, the geometry of (I) may be regarded as normal (Allen et al., 1995).
In the crystal of (I), an N—H···I hydrogen bond (Table 1) links the cation and the anion. A weak C—H···O interaction may also help to consolidate the packing, leading to [001] chains. There are no aromatic π-π stacking interactions in (I) as the closest centroid-centroid separation is greater than 4.37 Å.