Invariant and variable intermolecular interactions in functionalized malonic acid half-esters: X-ray, Hirshfeld surface and PIXEL energy analyses

Abstract

A series of functionalized malonic acid half-ester derivatives (parent compound MHE-1), with variations in functional groups at different positions on the aromatic ring, have been synthesized and crystal structures are determined at room temperature (296 K). The methyl IJ4-CH 3 , MHE-2) and chloro (4-Cl, MHE-3) derivatives are isomorphous with each other. The overall crystal packing of MHE-1-3 is similar. However, there are few differences observed between stacking of layers in these structures. Compounds with nitro IJ3-NO 2 , MHE-4) and ethyl ester IJ2-COOC 2 H 5 , MHE-5) substituents crystallize in different space groups and thus crystal packing is different when compared to MHE-1-3. In all the structures, intramolecular N-H⋯O and O-H⋯O hydrogen bonds generate a two fused SIJ6) ring motif. A detailed study is carried out to visualize intermolecular interactions observed in all five crystal structures (MHE-1-5) using Hirshfeld surface (HS) analysis with two dimensional fingerprint plots. The relative contribution of intermolecular H⋯H contacts in MHE-3 is substantially lower than that in MHE-1-2, though similar crystal packing arrangements of MHE-1-3 and MHE-2 and MHE-3 are isomorphous. From HS analysis it is clear that the observed H⋯H contact contribution (MHE-3) is a consequence of the presence of the chlorine substituent and growing contribution of Cl⋯H contacts. The relative contributions of other intermolecular contacts involving various atoms are comparable in MHE-1-3 structures. The intermolecular interaction energies are quantified using PIXEL for various molecular pairs extracted from respective crystal structures. Interestingly, there are some invariant and variable intermolecular contacts observed between different groups in all five structures.

Solution and Solid-State Photophysical Properties of Positional Isomeric Acrylonitrile Derivatives with Core Pyridine and Phenyl Moieties: Experimental and DFT Studies

“…The PIXEL method is an extremely useful tool to explore the nature of supramolecular interactions that crystal engineers regularly employ to design molecular crystals [ 83 , 84 , 85 , 86 , 87 , 88 ]. This method can also identify intermolecular interactions that are perceived as binding, but are in fact associated with repulsion (“antagonist synthons”), or interactions that are characterized by insignificant attractive or repulsive forces (“neutral synthons”).…”

Quantitative analysis of intermolecular interactions in 2,2’-((4-bromophenyl)methylene)bis(3-hydroxy-5,5-dimethylcyclohex-2-en-1-one): insights from crystal structure, PIXEL, Hirshfeld surfaces and QTAIM analysis

“…To quantify the energies associated with various intermolecular interactions present in the crystal structure of I, PIXEL calculation [35][36][37] was carried out as reported earlier. [38][39][40][41] Briefly, the distances involving hydrogen atoms are moved to their neutron values (C−H = 1.089 Å and O−H = 0.993 Å) and the resultant geometry used for the calculation. The electron density of the molecule has been obtained at the MP2/6-31G** level of theory using Gaussian 09.…”

Crystal and geometry-optimized structure, and Hirshfeld surface analysis of 1-(2-bromoethyl)indoline-2,3-dione

“…This analysis identified the various intermolecular contacts (O-H, H-H, C-H, C-C and H-Br) and their relative contributions in the crystal structure. The bond lengths (C-H = 1.083 Å , N-H = 1.009 Å and O-H = 0.983 Å ) were adjusted to typical neutron diffraction values before the HS calculation (Venkatesan et al, 2015(Venkatesan et al, , 2016a. In Hirshfeld surface diagrams, the contacts with distances shorter than the sum of the van der Waals radii are indicated as red and the contacts with distances longer than the van der Waals radii are represented as blue, whereas the contacts with distances equal to the sum of the van der Waals radii are indicated as white.…”