Effect of unwanted guest molecules on the stacking configuration of covalent organic frameworks: a periodic energy decomposition analysis

Abstract

Elucidating the precise stacking configuration of a covalent organic framework, COF, is critical to fully understand their various applications. Unfortunately, most COFs form powder crystals whose atomic characterisations are possible...

Origins of Offset-Stacking in Porous Frameworks

“…Our calculations for (COF1) 2 agree with previous theoretical studies that predict offsets of 1.4–2.8 Å that have been computed for this and other COFs, − ,− including COF-1 . Those studies were performed either using supramolecular DFT or sometimes with force fields, in the interest of using relatively large model systems.…”

“…In Figure S14a, one can observe a low-energy region corresponding to slip-stacking by ≈1.25 Å in any direction. This is the magnitude of the lateral offset that our calculations predict, relative to the eclipsed-cofacial or AA-stacking geometry, and it is similar to offsets of 1.4–2.8 Å that have been computed for this and other COFs, − ,− depending somewhat on the material and on the computational method. Lateral offsets of this magnitude are much smaller than what one would expect for AB-stacking, in which the vertices of one COF layer are centered within the voids of the adjacent layer.…”

“…In contrast to this rather consistent picture, a previous investigation of stacking interactions in a semi-infinite two-layer model of COF-1 concluded that offset-stacking is driven by electrostatics and dispersion, with no role for Pauli repulsion . This analysis was based on results from a periodic EDA applied to periodic PBE+D3/TZ2P calculations, which favor an offset of Δx = 1.8 Å and Δy = 3.3 Å at an interlayer separation of 3.1 Å .…”

“…Monomer units for these four systems are shown in Figure . We will also consider (COF1) 2 with a mesitylene molecule between the monomer units, as this has been suggested to change the structure from offset-stacking to eclipsed-cofacial stacking. − …”

“…The aim of the present work is to examine whether these same conclusions hold for macrocycles that assemble into porous frameworks in the solid state. For example, the [18]­annulene molecule (Figure b) packs in such a way that the π system of one monomer lies atop the pore of the neighboring monomer, in a form of offset-stacking. , The boron-based covalent organic framework (COF) material known as COF-1, a truncated “monomer” unit of which is shown in Figure d, forms alternating layers that may or may not have an offset, as the bulk materials are amorphous or polycrystalline and in some cases the microdomains are sensitive to the presence or absence of solvent molecules occupying the pore. − For applications in catalysis, it is desirable that the pores be accessible, but while it has been suggested that most COF materials exhibit eclipsed-cofacial stacking , (sometimes called “AA” stacking, borrowing the nomenclature used for graphene), , detailed analysis of powder diffraction along with theoretical calculations suggests that slipped- or offset-stacking (sometimes called “inclined stacking”) is common. − ,− The preference for eclipsed-cofacial (“AA”) versus fully staggered (“AB”) stacking may be controllable via functionalization …”