1,4-Diazacubane crystal structure rectified as piperazinium

Computational insight into the crystal structures of cubane and azacubanes

CONTEXT

Using quantum chemistry and atom-atom potential methods, the molecular and crystal structures of cubane 1 and all types of unsubstituted azacubanes 2-22 were calculated. Alternative possible polymorphs of cubane 1 have been proposed. The thermochemical properties of azacubanes in the gas and solid phases were assessed. Thermodynamic aspects of stability are considered, and a significant decrease in stability is revealed upon transition from cubane 1 to octaazacubane 22. It has been shown that the density and energetic properties of azacubanes depend nonlinearly on the number of nitrogen atoms in the structure and the density of octaazacubane 22 at room temperature is 1.546 g cm-3, which is significantly lower than the previously given estimate.

METHODS

In this work, DFT calculations were conducted through the software Gaussian 09 using B3LYP functional with basis set aug-cc-PVDZ and the Grimme dispersion correction D2. For crystal structure optimization, the atom-atom potential methods with PMC (packing of molecules in crystal) program were used. Charges for molecular electrostatic potential were fitted by FitMEP, and enthalpies of formation in gas phase were assessed by G3B3.

1-Azahomocubane

Highly strained cage hydrocarbons have long stood as fundamental molecules to explore the limits of chemical stability and reactivity, probe physical properties, and more recently as bioactive molecules and in materials discovery. Interestingly, the nitrogenous congeners have attracted much less attention. Previously absent from the literature, azahomocubanes, offer an opportunity to investigate the effects of a nitrogen atom when incorporated into a highly constrained polycyclic environment. Herein disclosed is the synthesis of 1-azahomocubane, accompanied by comprehensive structural characterization, physical property analysis and chemical reactivity. These data support the conclusion that nitrogen is remarkably well tolerated in a highly strained environment.

Pitfalls in the structural elucidation of small molecules. A critical analysis of a decade of structural misassignments of marine natural products

Covering: July 2010 to August 2021This article summarizes more than 200 cases of misassigned marine natural products reported between July 2010 and August 2021, sorting out errors according to the structural elements. Based on a comparative analysis of the original and the revised structures, major pitfalls still plaguing the structural elucidation of small molecules were identified, emphasizing the role of total synthesis, crystallography, as well as chemical- and biosynthetic logic to complement spectroscopic data. Distinct "trends" in natural product misassignment are evident between compounds of marine and plant origin, with an overall much lower incidence of "impossible" structures within misassigned marine natural products.

EBC-232 and 323: A Structural Conundrum Necessitating Unification of Five In Silico Prediction and Elucidation Methods

Structurally unique halimanes EBC-232 and EBC-323, isolated from the Australian rainforest plant Croton insularis, proved considerably difficult to elucidate. The two diastereomers, which consist an unusual oxo-6,7-spiro ring system fused to a dihydrofuran, were solved by unification and consultation of five in silico NMR elucidation and prediction methods [i.e., ACDLabs, olefin strain energy (OSE), DP4, DU8+ and TD DFT CD]. Structure elucidation challenges of this nature are prime test case examples for empowering future AI learning in structure elucidation.