Stacking (chemistry)

In chemistry, stacking refers to superposition of molecules or atomic sheets owing to attractive interactions between these molecules or sheets.

Metal dichalcogenides have the formula ME₂, where M = a transition metal and E = S, Se, Te.^[1] In terms of their electronic structures, these compounds are usually viewed as derivatives of M⁴⁺. They adopt stacked structures, which is relevant to their ability to undergo intercalation, e.g. by lithium, and their lubricating properties. The corresponding diselenides and even ditellurides are known, e.g., TiSe₂, MoSe₂, and WSe₂.

A combination of tetracyanoquinodimethane (TCNQ) and tetrathiafulvalene (TTF) forms a strong charge-transfer complex referred to as TTF-TCNQ.^[3] The solid shows almost metallic electrical conductance. In a TTF-TCNQ crystal, TTF and TCNQ molecules are arranged independently in separate parallel-aligned stacks, and an electron transfer occurs from donor (TTF) to acceptor (TCNQ) stacks.^[4]

Graphite consists of stacked sheets of covalently bonded carbon.^[5][6] The individual layers are called graphene. In each layer, each carbon atom is bonded to three other atoms forming a continuous layer of sp² bonded carbon hexagons, like a honeycomb lattice with a bond length of 0.142 nm, and the distance between planes is 0.335 nm.^[7] Bonding between layers is relatively weak van der Waals bonds, which allows the graphene-like layers to be easily separated and to glide past each other.^[8] Electrical conductivity perpendicular to the layers is consequently about 1000 times lower.^[9]

Linear chain compounds are materials composed of stacked arrays of metal-metal bonded molecules or ions. Such materials exhibit anisotropic electrical conductivity.^[10] One example is Rh(acac)(CO)₂ (acac = acetylacetonate, which stack with Rh···Rh distances of about 326 pm.^[11] Classic examples include Krogmann's salt and Magnus's green salt.

π–π stacking is a noncovalent interaction between the pi bonds of aromatic rings.^[12] Such "sandwich interactions" are however generally electrostatically repulsive. What is more commonly observed areeither a staggered stacking (parallel displaced) or pi-teeing (perpendicular T-shaped) interaction both of which are electrostatic attractive.^[13] For example, the most commonly observed interactions between aromatic rings of amino acid residues in proteins is a staggered stacked followed by a perpendicular orientation. Sandwiched orientations are relatively rare.^[14] Pi stacking is repulsive as it places carbon atoms with partial negative charges from one ring on top of other partial negatively charged carbon atoms from the second ring and hydrogen atoms with partial positive charges on top of other hydrogen atoms that likewise carry partial positive charges.^[15]

π–π interactions play a role in supramolecular chemistry, specifically the synthesis of catenane. The major challenge for the synthesis of catenane is to interlock molecules in a controlled fashion. Attractive π–π interactions exist between electron-rich benzene derivatives and electron-poor pyridinium rings.^[16] [2]Catanene was synthesized by treating bis(pyridinium) (A), bisparaphenylene-34-crown-10 (B), and 1, 4-bis(bromomethyl)benzene (C) (Fig. 2). The π–π interaction between A and B directed the formation of an interlocked template intermediate that was further cyclized by substitution reaction with compound C to generate the [2]catenane product.

• Noncovalent interaction
• Dispersion (chemistry)
• Cation–pi interaction
• Intercalation (biochemistry)
• Intercalation (chemistry)

• Luo R, Gilson HS, Potter MJ, Gilson MK (January 2001). "The physical basis of nucleic acid base stacking in water". Biophysical Journal. 80 (1): 140–148. Bibcode:2001BpJ....80..140L. doi:10.1016/S0006-3495(01)76001-8. PMC 1301220. PMID 11159389.
• Larry Wolf (2011): π-π (π-Stacking) interactions: origin and modulation