Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study

Abstract

Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.1(11,15).0(2,6).0(16,20))triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C(24)H(30)N(6)) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have P\bar 1 symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z', density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z' = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30-40 kJ mol(-1). These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in accordance with Ostwald's rule.

Revealing Non‐covalent Interactions in Molecular Crystals through Their Experimental Electron Densities

“…Van der Waals interactions : Proper modelling of van der Waals and, in particular, dispersion interactions is known to be difficult both in vacuo55 and in molecular crystals 11b. 24, 56 These interactions are due to time‐dependent perturbations of the ED and imply correlations among distant electrons.…”

“…For example, it is possible to analyze the contact geometries of atoms belonging to different molecules in the bulk, as they are retrieved by single crystal X-ray diffraction experiments, [10] looking for frequent packing modes and possible trends along chemically related substances [5] or by analysing such atom contacts in a more sophisticated and enlightening way by using the so-called Hirshfeld surfaces of the interacting molecules. [11] Interaction or packing energies, that is, the changes in the electronic energy of the molecule due to its gas-phase or crystalline surroundings, can be computed either quantum mechanically [12] or by suitable empirical atom-atom potentials, [13] and with a plethora of different recipes. [5,12] On top of this, the electron density (ED) observable 1(r), which may be obtained from ab initio methods as well as from single-crystal X-ray diffraction, contains a huge amount of information on how molecules in close contact influence each other and may thus be employed also for revealing intermolecular NCI.…”

Conformational flexibility of palladium BINAP complexes explored by X-ray analyses and DFT studies

“…However, to the best of knowledge, experimental and theoretical bite angles have not been compared. Different crystallographic isomorphs of conformational flexible macrocycles were studied in the solid state and the conversion reaction pathways by DFT [16]. We are interested in the construction of supramolecular arrangements based upon the BINAP palladium motif.…”

Rationalizing the Lacking of Inversion Symmetry in a Noncentrosymmetric Polar Racemate: An Experimental and Theoretical Study

“…The successful predictions yet made still use of database-stored information. In this respect, single-crystal X-ray diffraction analysis of complex systems represents a valuable and complementary approach to computer simulations 14 if specimens of sufficient quality are available. 15 …”