| Literature DB >> 35492285 |
Megan M Wysocki1, Gorana Puzovic1, Keith L Dowell1, Eric W Reinheimer2, Deidra L Gerlach1.
Abstract
The synthesis and the crystal structure of 1H-imidazole-1-methanol, C4H6N2O, are described. This compound comprises an imidazole ring with a methanol group attached at the 1-position affording an imine nitro-gen atom able to receive a hydrogen bond and an alcohol group able to donate to a hydrogen bond. This imidazole methanol crystallizes with monoclinic (P21/n) symmetry with three symmetry-unique mol-ecules. These three mol-ecules are connected via O-H⋯N hydrogen bonding in a head-to-tail configuration to form independent three-membered macrocycles. © Wysocki et al. 2022.Entities:
Keywords: crystal structure; hydrogen bonding; substituted imidazole
Year: 2022 PMID: 35492285 PMCID: PMC8983985 DOI: 10.1107/S2056989022002614
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The asymmetric unit of 1H-imidazole-1-methanol represented with displacement ellipsoids at the 50% probability level. Intermolecular hydrogen bonds are colored magenta with the three molecules colored and numbered for quick identity in the discussion. The coloring and numbering correspond to the numbering of the oxygen atom for each as follows: (1) light green, (2) orange, and (3) blue (if displayed or printed in grayscale: (1) lightest gray, (2) medium gray, and (3) darkest gray).
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| O1—H1⋯N4 | 0.82 | 1.93 | 2.741 (2) | 171 |
| O2—H2 | 0.82 | 1.94 | 2.753 (2) | 175 |
| O3—H3 | 0.91 (3) | 1.81 (3) | 2.715 (2) | 174 (2) |
Figure 2The packing arrangement of the three-molecule supermolecule with hydrogen bonds represented as dashed lines as viewed along the a axis of the unit cell. The approximate diameter of each three-member supermolecule is 9–9.5 Å with a height of about 2.6 Å.
Figure 3The packing arrangement of the three-molecule supermolecule with hydrogen bonds represented as dashed lines as viewed along the c axis of the unit cell. Observed at this angle is the π-stacking of molecule 1 with itself across an inversion center.
Figure 4The packing arrangement of the three-molecule supermolecule with hydrogen bonds represented as dashed lines as viewed along the b axis of the unit cell. The offset stacking of the three-membered supermolecule is due to the twofold screw axis orthogonal to this view.
Experimental details
| Crystal data | |
| Chemical formula | C4H6N2O |
|
| 98.11 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 293 |
|
| 10.6201 (8), 8.0201 (8), 18.2085 (16) |
| β (°) | 91.262 (7) |
|
| 1550.5 (2) |
|
| 12 |
| Radiation type | Mo |
| μ (mm−1) | 0.09 |
| Crystal size (mm) | 0.39 × 0.20 × 0.13 |
| Data collection | |
| Diffractometer | XtaLAB Mini II |
| Absorption correction | Analytical [multi-faceted crystal analytical numeric absorption correction (Clark & Reid, 1995 |
|
| 0.876, 1.000 |
| No. of measured, independent and observed [ | 10521, 2764, 1722 |
|
| 0.026 |
| (sin θ/λ)max (Å−1) | 0.597 |
| Refinement | |
|
| 0.041, 0.110, 1.02 |
| No. of reflections | 2764 |
| No. of parameters | 197 |
| No. of restraints | 3 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.11, −0.13 |
Computer programs: CrysAlis PRO (Rigaku OD, 2021 ▸), SHELXT2014/5 (Sheldrick, 2015a ▸), SHELXL2014/7 (Sheldrick, 2015b ▸), and OLEX2 (Dolomanov et al., 2009 ▸).
| C4H6N2O | |
| Melting point: 328 K | |
| Monoclinic, | Mo |
| Cell parameters from 945 reflections | |
| θ = 2.2–22.5° | |
| µ = 0.09 mm−1 | |
| β = 91.262 (7)° | |
| Plate, colourless | |
| 0.39 × 0.20 × 0.13 mm | |
| XtaLAB Mini II diffractometer | 2764 independent reflections |
| Radiation source: fine-focus sealed X-ray tube, Rigaku (Mo) X-ray Source | 1722 reflections with |
| Graphite monochromator | |
| Detector resolution: 10.0000 pixels mm-1 | θmax = 25.1°, θmin = 2.2° |
| ω scans | |
| Absorption correction: analytical [multi-faceted crystal analytical numeric absorption correction (Clark & Reid, 1995) and spherical harmonic empirical (using intensity measurements) absorption correction implemented in SCALE3 ABSPACK scaling algorithm] | |
| 10521 measured reflections |
| Refinement on | Hydrogen site location: mixed |
| Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
| (Δ/σ)max < 0.001 | |
| Δρmax = 0.11 e Å−3 | |
| 2764 reflections | Δρmin = −0.13 e Å−3 |
| 197 parameters | Extinction correction: SHELXL2014/7 (Sheldrick 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
| 3 restraints | Extinction coefficient: 0.0103 (17) |
| Primary atom site location: dual |
| Experimental. A clear, colorless platelike crystal of C4H6N2O was grown from a dioxane
reaction mixture slurry. The crystal of dimensions 0.39 x 0.20 x 0.13 mm was
mounted on MiTeGen loop with Parabar oil and diffraction data was collected.
The asymmetric unit includes three units of the C4H6N2O molecule. The
three crystallographically unique molecules are linked through hydrogen
bonding in a head-to-tail fashion creating the pseudo-superstructure
(C4H6N2O)3. Diffraction data was collected with a Rigaku XtaLAB Mini
II benchtop X-ray diffractometer with a fine-focus sealed Mo-target X-ray tube
(λ = 0.71073 Å) operated at 600 W power (50 kV, 12 mA) and a HyPix-Bantam
Hybrid Photon Counting (HPC) Detector. The X-ray intensities were measured at
293 (2) K; the detector was placed at a distance 4.50 cm from the crystal. The
collected frames were integrated with the CrysAlisPro 1.171.41.103a (Rigaku
Oxford Diffraction, 2020) software package using a narrow-frame algorithm.
Data were corrected for absorption effects using a multifaceted crystal
analytical numeric absorption correction (Clark & Reid, 1995) and spherical
harmonic empirical absorption correction implemented in the SCALE3 ABSPACK
scaling algorithm. The space group was assigned using the GRAL algorithm
within the CrysAlisPro 1.171.41.103a software package, solved with ShelXT
(Sheldrick, 2015a) and refined with ShelXL (Sheldrick, 2015b) and the
graphical interface Olex2 v1.3 (Dolomanov |
| Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
| O1 | 0.77310 (12) | 0.4000 (2) | 0.34750 (8) | 0.0820 (5) | |
| H1 | 0.7375 | 0.3864 | 0.3075 | 0.123* | |
| O3 | 0.13306 (15) | 0.3271 (2) | 0.40368 (8) | 0.0817 (5) | |
| O2 | 0.35971 (13) | 0.3114 (2) | 0.05475 (7) | 0.0858 (5) | |
| H2A | 0.3164 | 0.3045 | 0.0914 | 0.129* | |
| N1 | 0.58494 (13) | 0.40154 (18) | 0.41424 (8) | 0.0586 (4) | |
| N5 | 0.11264 (13) | 0.25149 (18) | 0.27851 (8) | 0.0561 (4) | |
| N3 | 0.56345 (14) | 0.29933 (19) | 0.10954 (9) | 0.0623 (4) | |
| N6 | 0.20362 (14) | 0.2999 (2) | 0.17339 (9) | 0.0685 (5) | |
| N2 | 0.38798 (15) | 0.3171 (2) | 0.41771 (10) | 0.0719 (5) | |
| N4 | 0.67175 (16) | 0.3827 (2) | 0.20794 (9) | 0.0797 (5) | |
| C10 | 0.21491 (16) | 0.2301 (2) | 0.23800 (11) | 0.0639 (5) | |
| H10 | 0.2861 | 0.1721 | 0.2541 | 0.077* | |
| C12 | 0.02984 (17) | 0.3416 (2) | 0.23675 (11) | 0.0652 (5) | |
| H12 | −0.0501 | 0.3765 | 0.2498 | 0.078* | |
| C8 | 0.64563 (18) | 0.4199 (2) | 0.08737 (12) | 0.0683 (6) | |
| H8 | 0.6546 | 0.4598 | 0.0398 | 0.082* | |
| C11 | 0.08636 (19) | 0.3702 (3) | 0.17301 (11) | 0.0698 (6) | |
| H11 | 0.0508 | 0.4296 | 0.1339 | 0.084* | |
| C2 | 0.46790 (19) | 0.4180 (3) | 0.38673 (11) | 0.0713 (6) | |
| H2 | 0.4457 | 0.4928 | 0.3496 | 0.086* | |
| C4 | 0.57914 (19) | 0.2808 (3) | 0.46627 (11) | 0.0715 (6) | |
| H4 | 0.6458 | 0.2406 | 0.4952 | 0.086* | |
| C6 | 0.5837 (2) | 0.2836 (3) | 0.18242 (12) | 0.0735 (6) | |
| H6 | 0.5395 | 0.2097 | 0.2116 | 0.088* | |
| C3 | 0.4592 (2) | 0.2309 (3) | 0.46797 (11) | 0.0724 (6) | |
| H3 | 0.4287 | 0.1490 | 0.4990 | 0.087* | |
| C7 | 0.71035 (19) | 0.4689 (3) | 0.14715 (14) | 0.0752 (6) | |
| H7 | 0.7729 | 0.5501 | 0.1477 | 0.090* | |
| C1 | 0.69704 (19) | 0.4933 (3) | 0.39245 (13) | 0.0814 (6) | |
| H1A | 0.6713 | 0.5942 | 0.3668 | 0.098* | |
| H1B | 0.7449 | 0.5258 | 0.4361 | 0.098* | |
| C9 | 0.0979 (2) | 0.2020 (3) | 0.35501 (12) | 0.0816 (7) | |
| H9A | 0.0106 | 0.1727 | 0.3628 | 0.098* | |
| H9B | 0.1488 | 0.1038 | 0.3650 | 0.098* | |
| C5 | 0.4684 (2) | 0.2148 (3) | 0.06467 (13) | 0.0879 (7) | |
| H5A | 0.5030 | 0.1893 | 0.0171 | 0.105* | |
| H5B | 0.4464 | 0.1103 | 0.0879 | 0.105* | |
| H3A | 0.218 (2) | 0.332 (3) | 0.4093 (12) | 0.102 (8)* |
| O1 | 0.0559 (9) | 0.1021 (11) | 0.0885 (10) | 0.0078 (8) | 0.0108 (7) | 0.0001 (9) |
| O3 | 0.0564 (10) | 0.1227 (13) | 0.0662 (9) | 0.0023 (8) | 0.0103 (7) | −0.0077 (9) |
| O2 | 0.0682 (10) | 0.1331 (13) | 0.0563 (8) | −0.0164 (9) | 0.0034 (7) | 0.0034 (9) |
| N1 | 0.0498 (9) | 0.0594 (9) | 0.0665 (10) | 0.0011 (8) | −0.0004 (7) | −0.0084 (9) |
| N5 | 0.0466 (9) | 0.0645 (10) | 0.0574 (9) | −0.0078 (7) | 0.0063 (7) | 0.0055 (8) |
| N3 | 0.0534 (9) | 0.0638 (10) | 0.0702 (11) | 0.0037 (8) | 0.0149 (8) | −0.0010 (9) |
| N6 | 0.0578 (10) | 0.0845 (12) | 0.0635 (11) | −0.0012 (9) | 0.0095 (8) | 0.0008 (9) |
| N2 | 0.0554 (10) | 0.0796 (11) | 0.0805 (12) | −0.0047 (9) | −0.0062 (9) | −0.0010 (10) |
| N4 | 0.0668 (11) | 0.0933 (13) | 0.0791 (12) | 0.0025 (9) | 0.0057 (9) | 0.0062 (11) |
| C10 | 0.0457 (11) | 0.0722 (13) | 0.0740 (13) | 0.0037 (10) | 0.0041 (9) | 0.0058 (11) |
| C12 | 0.0457 (11) | 0.0773 (13) | 0.0725 (13) | 0.0078 (10) | 0.0027 (10) | −0.0010 (11) |
| C8 | 0.0551 (12) | 0.0723 (14) | 0.0783 (14) | 0.0049 (11) | 0.0191 (11) | 0.0139 (12) |
| C11 | 0.0673 (13) | 0.0761 (14) | 0.0655 (13) | 0.0034 (11) | −0.0071 (10) | 0.0048 (11) |
| C2 | 0.0624 (13) | 0.0704 (13) | 0.0807 (14) | 0.0078 (11) | −0.0082 (11) | 0.0103 (12) |
| C4 | 0.0604 (13) | 0.0911 (16) | 0.0625 (12) | 0.0091 (11) | −0.0090 (9) | 0.0065 (12) |
| C6 | 0.0705 (13) | 0.0794 (14) | 0.0714 (14) | 0.0028 (10) | 0.0175 (10) | 0.0156 (11) |
| C3 | 0.0729 (14) | 0.0784 (14) | 0.0658 (13) | −0.0035 (12) | 0.0037 (10) | 0.0086 (11) |
| C7 | 0.0572 (12) | 0.0699 (14) | 0.0988 (17) | 0.0004 (11) | 0.0065 (12) | 0.0073 (13) |
| C1 | 0.0642 (13) | 0.0802 (14) | 0.1004 (16) | −0.0145 (12) | 0.0140 (11) | −0.0131 (13) |
| C9 | 0.0713 (14) | 0.1005 (17) | 0.0732 (14) | −0.0241 (12) | 0.0082 (11) | 0.0170 (14) |
| C5 | 0.0811 (16) | 0.0994 (17) | 0.0840 (15) | −0.0118 (14) | 0.0237 (12) | −0.0260 (14) |
| O1—H1 | 0.8200 | N4—C7 | 1.375 (2) |
| O1—C1 | 1.383 (2) | C10—H10 | 0.9300 |
| O3—C9 | 1.384 (3) | C12—H12 | 0.9300 |
| O3—H3A | 0.91 (3) | C12—C11 | 1.338 (2) |
| O2—H2A | 0.8200 | C8—H8 | 0.9300 |
| O2—C5 | 1.399 (3) | C8—C7 | 1.334 (3) |
| N1—C2 | 1.336 (2) | C11—H11 | 0.9300 |
| N1—C4 | 1.357 (2) | C2—H2 | 0.9300 |
| N1—C1 | 1.462 (2) | C4—H4 | 0.9300 |
| N5—C10 | 1.337 (2) | C4—C3 | 1.336 (3) |
| N5—C12 | 1.358 (2) | C6—H6 | 0.9300 |
| N5—C9 | 1.460 (2) | C3—H3 | 0.9300 |
| N3—C8 | 1.369 (2) | C7—H7 | 0.9300 |
| N3—C6 | 1.346 (2) | C1—H1A | 0.9700 |
| N3—C5 | 1.452 (3) | C1—H1B | 0.9700 |
| N6—C10 | 1.306 (2) | C9—H9A | 0.9700 |
| N6—C11 | 1.367 (2) | C9—H9B | 0.9700 |
| N2—C2 | 1.309 (2) | C5—H5A | 0.9700 |
| N2—C3 | 1.363 (2) | C5—H5B | 0.9700 |
| N4—C6 | 1.305 (3) | ||
| C1—O1—H1 | 109.5 | N1—C4—H4 | 126.6 |
| C9—O3—H3A | 110.9 (15) | C3—C4—N1 | 106.74 (17) |
| C5—O2—H2A | 109.5 | C3—C4—H4 | 126.6 |
| C2—N1—C4 | 106.01 (16) | N3—C6—H6 | 123.5 |
| C2—N1—C1 | 127.22 (18) | N4—C6—N3 | 113.06 (18) |
| C4—N1—C1 | 126.76 (17) | N4—C6—H6 | 123.5 |
| C10—N5—C12 | 106.44 (15) | N2—C3—H3 | 124.8 |
| C10—N5—C9 | 126.65 (17) | C4—C3—N2 | 110.35 (19) |
| C12—N5—C9 | 126.66 (16) | C4—C3—H3 | 124.8 |
| C8—N3—C5 | 127.10 (18) | N4—C7—H7 | 124.7 |
| C6—N3—C8 | 105.55 (17) | C8—C7—N4 | 110.6 (2) |
| C6—N3—C5 | 127.22 (17) | C8—C7—H7 | 124.7 |
| C10—N6—C11 | 104.29 (15) | O1—C1—N1 | 112.21 (16) |
| C2—N2—C3 | 104.31 (17) | O1—C1—H1A | 109.2 |
| C6—N4—C7 | 104.10 (18) | O1—C1—H1B | 109.2 |
| N5—C10—H10 | 123.8 | N1—C1—H1A | 109.2 |
| N6—C10—N5 | 112.49 (17) | N1—C1—H1B | 109.2 |
| N6—C10—H10 | 123.8 | H1A—C1—H1B | 107.9 |
| N5—C12—H12 | 126.9 | O3—C9—N5 | 112.38 (16) |
| C11—C12—N5 | 106.23 (17) | O3—C9—H9A | 109.1 |
| C11—C12—H12 | 126.9 | O3—C9—H9B | 109.1 |
| N3—C8—H8 | 126.6 | N5—C9—H9A | 109.1 |
| C7—C8—N3 | 106.73 (18) | N5—C9—H9B | 109.1 |
| C7—C8—H8 | 126.6 | H9A—C9—H9B | 107.9 |
| N6—C11—H11 | 124.7 | O2—C5—N3 | 112.05 (17) |
| C12—C11—N6 | 110.54 (18) | O2—C5—H5A | 109.2 |
| C12—C11—H11 | 124.7 | O2—C5—H5B | 109.2 |
| N1—C2—H2 | 123.7 | N3—C5—H5A | 109.2 |
| N2—C2—N1 | 112.59 (18) | N3—C5—H5B | 109.2 |
| N2—C2—H2 | 123.7 | H5A—C5—H5B | 107.9 |
| N1—C4—C3—N2 | 0.2 (2) | C4—N1—C2—N2 | 0.3 (2) |
| N5—C12—C11—N6 | 0.0 (2) | C4—N1—C1—O1 | 77.3 (2) |
| N3—C8—C7—N4 | −0.1 (2) | C6—N3—C8—C7 | 0.3 (2) |
| C10—N5—C12—C11 | 0.0 (2) | C6—N3—C5—O2 | 95.1 (2) |
| C10—N5—C9—O3 | 90.6 (2) | C6—N4—C7—C8 | −0.2 (2) |
| C10—N6—C11—C12 | 0.0 (2) | C3—N2—C2—N1 | −0.2 (2) |
| C12—N5—C10—N6 | 0.0 (2) | C7—N4—C6—N3 | 0.3 (2) |
| C12—N5—C9—O3 | −82.8 (2) | C1—N1—C2—N2 | 179.75 (16) |
| C8—N3—C6—N4 | −0.4 (2) | C1—N1—C4—C3 | −179.76 (17) |
| C8—N3—C5—O2 | −80.2 (2) | C9—N5—C10—N6 | −174.54 (17) |
| C11—N6—C10—N5 | 0.0 (2) | C9—N5—C12—C11 | 174.51 (18) |
| C2—N1—C4—C3 | −0.3 (2) | C5—N3—C8—C7 | 176.39 (18) |
| C2—N1—C1—O1 | −102.0 (2) | C5—N3—C6—N4 | −176.51 (19) |
| C2—N2—C3—C4 | 0.0 (2) |
| H··· | ||||
| O1—H1···N4 | 0.82 | 1.93 | 2.741 (2) | 171 |
| O2—H2 | 0.82 | 1.94 | 2.753 (2) | 175 |
| O3—H3 | 0.91 (3) | 1.81 (3) | 2.715 (2) | 174 (2) |