The overall goal of this experiment is to perform unique super molecular clusters selectively and characterize their symmetric features. This method can help answer key questions in the face of super molecular chemistry such as designs of super molecules with specific symmetry. The main advantage of this technique is that structures or symmetry of any super molecule is predictable from structures of their components.
To prepare binary organic salts, dissolve triphenylacetic acid or TPAA and the primary amine, either n butylamine, isobutylamine, t-butylamine, or t-amylamine together in 20 milliliters of methanol in a TPAA to amine molar ratio of one to one. See the text protocol for preparation in the case of turnery organic salts. Evaporate all of the solutions by rotary evaporators, affording the organic salts.
To prepare single crystals composed of super molecular clusters, dissolve five point zero milligrams of each of the organic salts in a glass vial in zero point three zero milliliters of toluene as a nonpolar good solvent. Toluene was selected because the super molecular clusters are preferably constructed in a nonpolar environment. For the organic salts, heat toluene up to 40 degrees Celsius to dissolve them.
Add hexane to the solution of the organic salts as a poor solvent to decrease solubility of the organic salt, except for the solution of the organic salt, TPAA t-butylamine. Keep the solution stable at room temperature in the glass vial, affording single crystals within a day. Measure foye transform infrared spectra to confirm the organic salt formation as described in the text protocol.
Pick up a high quality single crystal of the organic salt TPAA t-amylamine with a size around zero point three to one millimeter without cracks, which looks uniform under a stereomicroscope. A uniform crystal is not assemblies of multiple crystals, but a single crystal. Transfer the crystal from the glass vial into paraffin on a glass plate.
Put the single crystal on a loop. Set the loop with the single crystal in single crystal x-ray diffraction equipment. Start preparatory measurement of single crystal x-ray diffraction to collect x-ray diffraction patterns using the single crystal x-ray diffraction equipment as described in the text protocol.
Then, start regular measurement of single crystal x-ray diffraction to similarly collect x-ray diffraction patterns using the single crystal x-ray diffraction equipment as described in the text protocol. After solving the crystal structure as described in the text protocol, investigate the super molecular clusters in the crystal structures by computer graphics using Mercury software. Determine point group symmetries of hydrogen bonding patterns in the super molecular clusters by comparing the obtained patterns with the previously classified ones.
Characterize polyhedral features of the super molecular clusters in each of the crystal structures of the organic salts. First, delete all of the atoms in the super molecular clusters except for carbon and nitrogen atoms of the component carboxylate anions and ammonium cations. Then, make bonds between the carbon and nitrogen atoms of which original carboxylate and ammonium cations are connected by hydrogen bonds using Pimal Software.
Measure distances between carbon carbon and nitrogen nitrogen atoms and set boundaries for making further bonds. Make further bonds between carbon carbon atoms of which distances are less than five point four angstroms and nitrogen nitrogen atoms, of which distances are less than four point two angstroms. Determine the resulting polyhedrons from the organic salts by considering rotational axis, as well as numbers of sides of the polyhedron.
Here, TPAA isobutylamine forms a trans bicapped octahedron while TPAA t-butylamine, TPAA amylamine, TPAA isobutylamine t-butylamine, and TPAA isobutylamine t-amylamine form triangular dodecahedrons. Make additional bonds to the resulting polyhedrons from the organic salts by considering the number of sides, symmetry elements, and intermolecular interactions in the super molecular clusters. Determine the polyhedron of the TPAA n butylamine salt as square antiprism, by making two addition bonds due to its C-2 symmetry and 14 original bonds.
Determine the other polyhedrons of the organic salts TPAA n butylamine t-butylamine and TPAA n butylamine t-amylamine as triangular dodecahedron based on their C-2 symmetry and bands of trityl groups around the super molecular cluster. Representative results of single crystal x-ray analysis are shown here. Symmetry analysis on the super molecular clusters reveal their structural features as analogs of octocoordinated polyhedrons.
After watching this video, you should have a good understanding of how to characterize super molecules from a viewpoint of symmetry.
