| Literature DB >> 21577537 |
Turganbay S Iskenderov, Irina A Golenya, Elźbieta Gumienna-Kontecka, Igor O Fritsky, Elena V Prisyazhnaya.
Abstract
The title structure, C(9)H(11)N(3)O(2), is a racemate. The chiral centre is situated at the N-C-N C atom of the imidazolidine ring. The inter-planar angle between the mean planes of the pyridine and imidazolidine rings is 89.41 (5)°. The methyl group is in a trans position with respect to the pyridine N atom. In the crystal, the mol-ecules are arranged in zigzag layers parallel to the b axis. The mol-ecules within the layers are inter-connected by strong O-H⋯N and weak N-H⋯O hydrogen bonds; the former take place between OH groups and amine N atoms and the latter between the amine N atom and the carbonyl O atom. In addition, C-H⋯O inter-actions are also present.Entities:
Year: 2009 PMID: 21577537 PMCID: PMC2970069 DOI: 10.1107/S1600536809030840
Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN: 1600-5368
| C9H11N3O2 | |
| Monoclinic, | Mo |
| Hall symbol: -P 2ybc | Cell parameters from 505 reflections |
| θ = 4.5–27.0° | |
| µ = 0.11 mm−1 | |
| β = 106.43 (3)° | Block, colourless |
| 0.25 × 0.17 × 0.12 mm | |
| Kuma KM-4-CCD diffractometer | 2048 independent reflections |
| Radiation source: fine-focus sealed tube | 1772 reflections with |
| graphite | |
| ω scans | θmax = 28.4°, θmin = 3.4° |
| Absorption correction: multi-scan ( | |
| 6025 measured reflections |
| Refinement on | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: difference Fourier map |
| H atoms treated by a mixture of independent and constrained refinement | |
| (Δ/σ)max < 0.001 | |
| 2048 reflections | Δρmax = 0.31 e Å−3 |
| 137 parameters | Δρmin = −0.21 e Å−3 |
| 0 restraints | Extinction correction: |
| 35 constraints | Extinction coefficient: 0.011 (3) |
| Primary atom site location: structure-invariant direct methods |
| 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 |
| O1 | 0.16520 (11) | 0.16310 (8) | 0.36523 (9) | 0.0161 (2) | |
| O2 | 0.40231 (11) | 0.01414 (8) | 0.28974 (9) | 0.0197 (2) | |
| N1 | 0.33317 (13) | 0.31162 (10) | 0.12474 (10) | 0.0143 (2) | |
| N2 | 0.02391 (13) | 0.16898 (10) | 0.05476 (10) | 0.0162 (2) | |
| N3 | 0.27351 (13) | 0.20590 (10) | 0.29470 (10) | 0.0135 (2) | |
| C1 | 0.21832 (17) | 0.43456 (12) | 0.27885 (13) | 0.0175 (3) | |
| H1A | 0.1455 | 0.4293 | 0.3351 | 0.026* | |
| H1B | 0.1815 | 0.5026 | 0.2179 | 0.026* | |
| H1C | 0.3330 | 0.4496 | 0.3307 | 0.026* | |
| C2 | 0.21024 (15) | 0.31194 (11) | 0.20447 (11) | 0.0137 (3) | |
| C3 | 0.03258 (15) | 0.27995 (11) | 0.11645 (11) | 0.0137 (3) | |
| C4 | 0.36622 (15) | 0.12145 (12) | 0.24864 (12) | 0.0147 (3) | |
| C5 | 0.41829 (16) | 0.18664 (12) | 0.14047 (12) | 0.0167 (3) | |
| H5A | 0.5407 | 0.1966 | 0.1638 | 0.020* | |
| H5B | 0.3818 | 0.1385 | 0.0598 | 0.020* | |
| C6 | −0.10579 (17) | 0.36021 (12) | 0.09906 (13) | 0.0184 (3) | |
| H6 | −0.0958 | 0.4360 | 0.1446 | 0.022* | |
| C7 | −0.25965 (17) | 0.32455 (13) | 0.01199 (13) | 0.0206 (3) | |
| H7 | −0.3546 | 0.3762 | −0.0018 | 0.025* | |
| C8 | −0.26922 (16) | 0.21144 (13) | −0.05353 (13) | 0.0196 (3) | |
| H8 | −0.3702 | 0.1859 | −0.1130 | 0.023* | |
| C9 | −0.12508 (16) | 0.13664 (12) | −0.02886 (12) | 0.0177 (3) | |
| H9 | −0.1323 | 0.0601 | −0.0727 | 0.021* | |
| H1O | 0.229 (3) | 0.1711 (18) | 0.454 (2) | 0.049 (6)* | |
| H1N | 0.409 (2) | 0.3703 (16) | 0.1556 (15) | 0.023 (4)* |
| O1 | 0.0174 (5) | 0.0199 (5) | 0.0126 (4) | −0.0039 (3) | 0.0067 (4) | 0.0010 (3) |
| O2 | 0.0196 (5) | 0.0154 (5) | 0.0233 (5) | 0.0026 (3) | 0.0050 (4) | 0.0021 (4) |
| N1 | 0.0146 (5) | 0.0152 (5) | 0.0135 (5) | −0.0028 (4) | 0.0049 (4) | −0.0007 (4) |
| N2 | 0.0169 (5) | 0.0145 (5) | 0.0166 (5) | −0.0009 (4) | 0.0040 (4) | −0.0016 (4) |
| N3 | 0.0147 (5) | 0.0148 (5) | 0.0117 (5) | −0.0010 (4) | 0.0052 (4) | 0.0016 (4) |
| C1 | 0.0208 (7) | 0.0143 (6) | 0.0172 (6) | −0.0012 (5) | 0.0052 (5) | −0.0020 (5) |
| C2 | 0.0165 (6) | 0.0132 (6) | 0.0118 (6) | 0.0003 (4) | 0.0046 (5) | 0.0010 (4) |
| C3 | 0.0162 (6) | 0.0139 (6) | 0.0117 (6) | −0.0012 (4) | 0.0050 (5) | 0.0011 (4) |
| C4 | 0.0111 (6) | 0.0170 (6) | 0.0139 (6) | −0.0022 (4) | −0.0001 (4) | −0.0033 (5) |
| C5 | 0.0161 (6) | 0.0186 (6) | 0.0160 (6) | 0.0012 (5) | 0.0057 (5) | −0.0010 (5) |
| C6 | 0.0211 (7) | 0.0155 (6) | 0.0187 (6) | 0.0025 (5) | 0.0060 (5) | −0.0019 (5) |
| C7 | 0.0173 (7) | 0.0221 (7) | 0.0216 (7) | 0.0063 (5) | 0.0042 (5) | 0.0027 (5) |
| C8 | 0.0156 (6) | 0.0236 (7) | 0.0171 (6) | −0.0009 (5) | 0.0008 (5) | 0.0017 (5) |
| C9 | 0.0194 (7) | 0.0161 (6) | 0.0167 (6) | −0.0022 (5) | 0.0036 (5) | −0.0029 (5) |
| O1—N3 | 1.3917 (13) | C1—H1C | 0.9600 |
| O1—H1O | 0.95 (2) | C2—C3 | 1.5316 (18) |
| O2—C4 | 1.2250 (16) | C3—C6 | 1.3891 (17) |
| N1—C5 | 1.4854 (16) | C4—C5 | 1.5047 (17) |
| N1—C2 | 1.4907 (16) | C5—H5A | 0.9700 |
| N1—H1N | 0.874 (17) | C5—H5B | 0.9700 |
| N2—C9 | 1.3376 (17) | C6—C7 | 1.3908 (19) |
| N2—C3 | 1.3395 (16) | C6—H6 | 0.9300 |
| N3—C4 | 1.3536 (16) | C7—C8 | 1.3783 (19) |
| N3—C2 | 1.4744 (16) | C7—H7 | 0.9300 |
| C1—C2 | 1.5139 (17) | C8—C9 | 1.3863 (19) |
| C1—H1A | 0.9600 | C8—H8 | 0.9300 |
| C1—H1B | 0.9600 | C9—H9 | 0.9300 |
| N3—O1—H1O | 104.8 (12) | C6—C3—C2 | 123.14 (11) |
| C5—N1—C2 | 108.08 (9) | O2—C4—N3 | 126.10 (12) |
| C5—N1—H1N | 109.4 (11) | O2—C4—C5 | 127.42 (11) |
| C2—N1—H1N | 107.8 (10) | N3—C4—C5 | 106.47 (11) |
| C9—N2—C3 | 117.59 (11) | N1—C5—C4 | 105.65 (10) |
| C4—N3—O1 | 119.32 (10) | N1—C5—H5A | 110.6 |
| C4—N3—C2 | 113.53 (10) | C4—C5—H5A | 110.6 |
| O1—N3—C2 | 116.04 (9) | N1—C5—H5B | 110.6 |
| C2—C1—H1A | 109.5 | C4—C5—H5B | 110.6 |
| C2—C1—H1B | 109.5 | H5A—C5—H5B | 108.7 |
| H1A—C1—H1B | 109.5 | C3—C6—C7 | 118.43 (12) |
| C2—C1—H1C | 109.5 | C3—C6—H6 | 120.8 |
| H1A—C1—H1C | 109.5 | C7—C6—H6 | 120.8 |
| H1B—C1—H1C | 109.5 | C8—C7—C6 | 119.00 (12) |
| N3—C2—N1 | 101.45 (9) | C8—C7—H7 | 120.5 |
| N3—C2—C1 | 111.05 (10) | C6—C7—H7 | 120.5 |
| N1—C2—C1 | 111.28 (10) | C7—C8—C9 | 118.60 (12) |
| N3—C2—C3 | 109.17 (10) | C7—C8—H8 | 120.7 |
| N1—C2—C3 | 109.38 (9) | C9—C8—H8 | 120.7 |
| C1—C2—C3 | 113.79 (10) | N2—C9—C8 | 123.35 (12) |
| N2—C3—C6 | 123.02 (12) | N2—C9—H9 | 118.3 |
| N2—C3—C2 | 113.82 (10) | C8—C9—H9 | 118.3 |
| C4—N3—C2—N1 | −23.00 (12) | N1—C2—C3—C6 | −120.73 (13) |
| O1—N3—C2—N1 | −166.82 (9) | C1—C2—C3—C6 | 4.41 (17) |
| C4—N3—C2—C1 | −141.35 (11) | O1—N3—C4—O2 | −21.10 (17) |
| O1—N3—C2—C1 | 74.84 (13) | C2—N3—C4—O2 | −163.63 (11) |
| C4—N3—C2—C3 | 92.40 (12) | O1—N3—C4—C5 | 160.17 (9) |
| O1—N3—C2—C3 | −51.42 (13) | C2—N3—C4—C5 | 17.65 (13) |
| C5—N1—C2—N3 | 18.56 (12) | C2—N1—C5—C4 | −9.58 (12) |
| C5—N1—C2—C1 | 136.75 (10) | O2—C4—C5—N1 | 176.85 (11) |
| C5—N1—C2—C3 | −96.68 (11) | N3—C4—C5—N1 | −4.45 (13) |
| C9—N2—C3—C6 | 1.26 (18) | N2—C3—C6—C7 | −1.06 (19) |
| C9—N2—C3—C2 | −176.93 (11) | C2—C3—C6—C7 | 176.96 (11) |
| N3—C2—C3—N2 | −52.74 (13) | C3—C6—C7—C8 | 0.01 (19) |
| N1—C2—C3—N2 | 57.46 (13) | C6—C7—C8—C9 | 0.7 (2) |
| C1—C2—C3—N2 | −177.41 (10) | C3—N2—C9—C8 | −0.43 (19) |
| N3—C2—C3—C6 | 129.08 (12) | C7—C8—C9—N2 | −0.6 (2) |
| H··· | ||||
| O1—H1O···N1i | 0.95 (2) | 1.78 (2) | 2.7287 (16) | 175.5 (18) |
| N1—H1N···O2ii | 0.874 (17) | 2.135 (18) | 3.0058 (15) | 173.7 (15) |
| C6—H6···O1iii | 0.93 | 2.47 | 3.2867 (17) | 147 |
| C7—H7···O2iii | 0.93 | 2.81 | 3.3559 (17) | 119 |
| C8—H8···O2iv | 0.93 | 2.80 | 3.4177 (17) | 125 |
Hydrogen-bond geometry (Å, °)
| H⋯ | ||||
|---|---|---|---|---|
| O1—H1 | 0.95 (2) | 1.78 (2) | 2.7287 (16) | 175.5 (18) |
| N1—H1 | 0.874 (17) | 2.135 (18) | 3.0058 (15) | 173.7 (15) |
| C6—H6⋯O1iii | 0.93 | 2.47 | 3.2867 (17) | 147 |
| C7—H7⋯O2iii | 0.93 | 2.81 | 3.3559 (17) | 119 |
| C8—H8⋯O2iv | 0.93 | 2.80 | 3.4177 (17) | 125 |
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .