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

Abstract

The total charge density of PYRAC, a polar (Pca21) organic racemate with Z' = 2 was derived from high-resolution single-crystal X-ray diffraction data at T = 100(2) K and periodic DFT calculations.The PYRAC asymmetric unit consists of a hydrogen-bonded pair of conformationally different enantiomers, A and Bi, where the subscript 'i' indicates a reversed absolute configuration. The lattice stability was compared with that of centrosymmetric possibly competing structures, with the aim of understanding why a non-centrosymmetric lattice framework is obtained from a racemic mixture. The likelihood of specific intermolecular recognition processes among different conformers of PYRAC in the very first stages of nucleation was investigated by DFT simulations in vacuo. Two competing, equivalent interconversion pseudorotatory paths between the most stable A and the least stable B conformers were found. It results that molecules spend most of their time (≈ 53 %) in the A conformation, while the B one is far less populated (≈ 7 %). Therefore, centrosymmetric AAi adducts are formed very frequently in the reaction liquor, while the BBi ones are rare. Nevertheless, AAi pairs produce crystal forms with cohesive energies and densities significantly less favourable than those estimated for the non-centrosymmetric heterochiral ABi ones. Therefore, preference for Z' = 2 in conjunction with non-centrosymmetric point and space groups results from the thermodynamic control of the crystallization process. The capability of forming extended hydrogen bond chains throughout the lattice appears to be a prerequisite to bind together the fundamental ABi repeating units.

Two-component organic crystals without hydrogen bonding: structure and intermolecular interactions in bimolecular stacking

“…If yes, a significant thermodynamic drive toward heterorecognition might be safely assumed, implying that strongly associated AB pairs might act as effective supramolecular synthons. 40,41 This is indeed the case for structures in the current NOHB-ENE dataset. Individual molecule-molecule pair energies were extracted from PIXEL lattice calculations and ranked according to their magnitude (highest to lowest).…”

“…The alternate-ladder motif AL predominates except for the cocrystal with pyrene (8); due to the ovoidal shape of the hydrocarbon coformer ( Figure 8b) the elongation axes are not strictly parallel, resulting in a slanted column SC motif. In our calculations for TCNB (41) and even more TCNQ (42) nearly all complexes show very moderately stabilizing or actually destabilizing dispersive and Coulombic packing excess energies (Figure 9). Unless some energetic mechanism escaping our simulation is at work, a rationalization of the apparent…”

“…Interplanar separation R (Å), and dimerization energies (kJ·mol -1 ) of stacked hetero-dimers extracted from the crystal structures of TCNB(41) and TCNQ (42) cocrystals. The packing motif is alternate ladder (AL,…”

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

“…RDF or orientation angle comparisons become less indicative. It can never be neglected that the relative motions of rigid groups in floppy molecules (Lo Presti et al, 2014;Gionda et al, 2018) cause apparent fluctuations, and sometimes significant shifts, of the c.o.m. coordinates.…”

“…To fill this gap, a new sequence of computer programs, the CLPdyncry suite, has been designed explicitly for application to the condensed states of small organic molecules, and has recently been applied with quantitative success to liquids and liquid droplets (Gavezzotti & Lo Presti, 2019). Along with standard MD algorithms, the suite includes an intermolecular force field called AA-CLP (atom-atom Coulomb-London-Pauli) (Gavezzotti, 2013(Gavezzotti, , 2011 that has been shown to be a versatile tool for the static or Monte Carlo simulation of organic crystals (Gavezzotti & Lo Presti, 2015Gavezzotti et al, , 2018Colombo et al, 2017;Lo Presti, 2014, 2018. Incidentally, its functional form cannot be adapted to any of the currently available environments, as the intermolecular part of its potential is generated for each different molecule from general atomic and molecular parameters (Gavezzotti, 2011).…”