The structure of 2-[(4-chlorophenylazo) cyanomethyl] benzoxazole, C15H9ClN4O (I), has triclinic (
Benzoxazole derivatives are one of the most important bioactive heterocyclic organic compounds in pharmaceutical chemistry. They have been used as a starting material for synthesis of bioactive structures of pharmaceutical drugs, such as the antibiotic Calcimycin that includes a 2-substituted benzoxazole ring in its molecular structure [
It was reported that knowing the crystal structure and conformation of 2-substituted benzoxazole derivatives supports important information for predicting their mode of orientation on the receptor [
In view of the aforementioned literature survey and to support the pharmaceutical and organic chemistry scientists with structural aspects that may be of value in designing new derivatives and potent drugs, we present the geometrical, stereochemical features of two bioactive 2-substituted benzoxazole derivatives comparing their structures with each other and related structures, using X-ray single crystal analysis and molecular mechanics (MM) calculations. The chosen derivatives are 2-[(4-chlorophenylazo) cyanomethyl] benzoxazole, C15H9ClN4O (I) and 2-[(arylidene) cyanomethyl] benzoxazole, C17H10N2O3 (II).
The target compounds have been prepared according to the reported procedure [
Chemical diagram of the target compounds.
Crystals were selected and checked for imperfections such as cracks, bubbles, twining, or voids and mounted onto thin glass fibers and glued with epoxy glue. X-ray diffraction data were collected at room temperature on an Enraf-Nonius 590 Kappa CCD single crystal diffractometer with graphite monochromated Mo-K
Crystal data of the studied compounds.
(I) | (II) | |
---|---|---|
Crystal data | ||
Chemical formula | C15H9ClN4O | C17H10N2O3 |
|
296.72 | 290.28 |
Crystal system, space group | Triclinic, |
Triclinic, |
Temperature (K) | 298 | 298 |
|
7.5050 (7), 7.4836 (10), 13.4301 (17) | 7.4919 (5), 13.0828 (9), 14.1914 (14) |
|
106.488 (6), 90.485 (7), 102.759 (8) | 94.355 (3), 101.180 (3), 102.504 (6) |
|
703.37 (15) | 1322.07 (19) |
|
2 | 4 |
Radiation type | Mo |
Mo |
|
0.28 | 0.10 |
Crystal size (mm) | 0.12 × 0.10 × 0.09 | 0.12 × 0.11 × 0.08 |
|
||
Data collection | ||
Absorption correction | Multiscan | Multiscan |
|
0.97, 0.98 | 0.99, 0.99 |
Number of measured, independent and observed |
4166, 3007, 1543 | 7240, 4861, 2163 |
|
0.031 | 0.084 |
|
0.655 | 0.617 |
|
||
Refinement | ||
|
0.071, 0.070, 1.13 | 0.089, 0.155, 0.97 |
Number of reflections, parameters, and restraints | 1309, 64, 0 | 1738, 133, 0 |
|
0.25, −0.26 | 0.33, −0.25 |
The crystal structures were solved using Superflip [
The crystal data is listed in Table
Molecular mechanics
Structures of compounds (I) and (II) consist mainly of benzoxazole connected with different chemical moieties at C7 (Figures
The 50% probability displacement ellipsoids representation of compound (I).
The 50% probability displacement ellipsoids representation of compound (II).
Benzoxazole is almost planar, where the maximum deviation from the mean plane corresponds to the atom C2, −0.013 (3) Å in (I) and the atoms C6, 0.008 (6) Å and O4, −0.012 (4) Å, in (IIa) and (IIb), respectively. This is comparable with the reported structures which have the same moiety, such as 2-(4-aminophenyl)-1, 3-benzoxazole [
In compound (II), the benzoxazole group is linked to benzodioxol via acrylonitrile moiety. Planar configuration of benzodioxole moiety in (IIb) is confirmed by the deviation of the benzodioxole atoms from their best plane, with maximum deviation at O6, −0.026 (4) Å. However, in (IIa), the dioxole ring adopts the envelope conformation with C17 deviating from the plane defined by the rest of the atoms of the ring (O2-C17) by −0.069 (7) Å. The puckering parameters [
Conformational investigation of the structures reveals that there is cisoid conformation between the cyano group and benzoxazole nitrogen in compound (II) (Figure
The structures are stabilized by the intermolecular interactions and a network of hydrogen bond contacts conformed parallel layers, N-H
Hydrogen-bond geometry (
D–H |
|
H |
D |
D–H |
---|---|---|---|---|
N1–H11 |
0.950 | 1.975 | 2.710 (4) | 133 |
Hydrogen-bond geometry (
D–H |
D–H | H |
D |
D–H |
---|---|---|---|---|
C13–H131 |
0.950 | 2.519 | 3.431 (8) | 161 |
C16–H161 |
0.950 | 2.600 | 3.450 (8) | 149 |
C16–H161 |
0.950 | 2.433 | 3.063 (8) | 124 |
C30–H301 |
0.950 | 2.574 | 3.464 (8) | 156 |
C33–H331 |
0.950 | 2.426 | 3.052 (8) | 123 |
Symmetry code:
The molecular packing of (I).
The molecular packing of (II) with the intermolecular interactions shown as dashed line.
The minimum energy structure obtained by molecular mechanics of the investigated compounds did not match well the crystal structures obtained experimentally, Figures
Superimposition view of the calculated structure (black) on the X-ray structure (gray) for the compound (I).
Superimposition view of the calculated structure (black) on the X-ray structure (gray) for the compound (II).
Tables
Selected geometrical values of molecular mechanics and experimentally obtained structures of compound (I).
Bond length |
Exp. | MM | Bond angles (°) | Exp. | MM |
---|---|---|---|---|---|
N1–N2 | 1.317 (3) | 1.354 | C1–C2–C3 | 117.1 (3) | 117.07 |
N2–C8 | 1.307 (4) | 1.3485 | C3–C4–C5 | 121.6 (3) | 121.17 |
C8–C9 | 1.434 (4) | 1.31 | O1–C7–N4 | 115.7 (3) | 115.84 |
C1–C2 | 1.381 (4) | 1.390 | Cl1–C13–C14 | 119.6 (3) | 119.9 |
C6–C1 | 1.387 (4) | 1.384 | C6–O1–C7–C8 | 179.5 (4) | 180 |
Cl1–C13 | 1.737 (3) | 1.726 | C10–N1–N2–C8 | 179.1 (5) | 179.99 |
C10–C11 | 1.375 (4) | 1.398 | C7–C8–C9–N3 | 130 (2) | 180 |
C11–C12 | 1.395 (4) | 1.398 | C5–C6–C1–N4 | 179.6 (5) | 180 |
C13–C12 | 1.369 (5) | 1.396 | N2–N1–C10–C15 | 179.9 (5) | 0 |
C13–C14 | 1.389 (5) | 1.396 | H1–N1–C10–C11 | 177.5 (8) | 0 |
N4–C1 | 1.400 (4) | 1.348 | H1–N1–C10–C15 | 1.0 (8) | 180 |
N4–C7 | 1.294 (4) | 1.358 | C10–N1–H1–N4 | 179.7 (13) | 180 |
Selected geometrical values of molecular mechanics and experimentally obtained structures of compound (II).
Bond length |
Exp. | MM | Bond angles (°) | Exp. | MM |
---|---|---|---|---|---|
N1–C6 | 1.403 (5) | 1.348 | C1–C6–C5 | 120.7 (4) | 121.59 |
N1–C7 | 1.279 (5) | 1.363 | C9–C8–C7 | 112.1 (4) | 112.90 |
C6–C5 | 1.366 (5) | 1.390 | C8–C10–C11 | 131.3 (4) | 221.59 |
C6–C1 | 1.378 (5) | 1.381 | C13–C14–C15 | 123.1 (5) | 122.58 |
C1–C2 | 1.372 (6) | 1.390 | O2–C17–O3 | 107.6 (3) | 105.35 |
C5–C4 | 1.373 (6) | 1.399 | C13–C12–C11 | 117.6 (4) | 116.18 |
C4–C3 | 1.395 (6) | 1.403 | C7–O1–C1–C2 | 179.8 (9) | 180 |
N2–C9 | 1.132 (1) | 1.15 | O1–C1–C2–C3 | 179.8 (11) | 180 |
C9–C8 | 1.423 (6) | 1.321 | C7–N1–C6–C5 | 179.0 (10) | 180 |
C7–C8 | 1.460 (5) | 1.345 | N1–C7–C8–C9 | 4.2 (6) | 0 |
C11–C12 | 1.419 (5) | 1.417 | C11–C10–C8–C7 | 178.1 (11) | 0 |
C10–C11 | 1.446 (5) | 1.353 | C13–C12–C11–C10 | −179.2 (10) | 179.99 |
However, the energy of the experimental structures was higher than the energy of the structure obtained using molecular mechanics by the values 5.8 kcal·mol−1 in compound (I) and 1.9 kcal·mol−1 in compound (II). This variation may be due to the fact that the experimental structure of the investigated compounds in crystal conditions (i.e., the neighbouring molecules, hydrogen bonding, and other nonbonded interactions in the crystal lattice environment) is taken into account. This is in agreement with what was reported in the literature showing that the effects of hydrogen-bonding and van der Waals interactions in the crystal structure cause the molecules to adopt higher-energy conformations, which correspond to local minima in the molecular potential energy surface [
Crystallographic and stereochemical study of 2-substituted benzoxazole derivatives, 2-[(4-chlorophenylazo) cyanomethyl] benzoxazole and 2-[(arylidene) cyanomethyl] benzoxazole, has been introduced using X-ray single crystal and MM. The study has reported that the crystal structures of the two compounds have a triclinic (
The authors declare that there is no conflict of interests regarding the publication of this paper.
This work is one of the seeds Professor Naima Abdel-Kader Ahmed (Crystallography Laboratory, NRC, Egypt) has planted, so the authors would like to offer a thank you to her kind soul. The authors thank the Pharmaceutical Chemistry Group, Faculty of Pharmacy, University of Alexandria, Egypt, for the great help.