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Stacking (chemistry)

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Stacking in supramolecular chemistry refers to a stacked arrangement of oftenaromatic molecules, which is adopted due to interatomic interactions. The most common example of a stacked system is found for consecutive base pairs in DNA. Stacking also frequently occurs in proteins where two relatively non-polar rings overlap. Which Intermolecular forces contribute to stacking is a matter of debate.

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Crystal structure of a trinitrofluorene bound inmolecular tweezers through aromatic stacking interactions. Reported by Lehn and coworkers.^[1]

Controlling ForcesStacking is often referred to as π-π interaction, though effects due to the presence of a π-orbital are only one source of such interactions, and in many common cases appear not to be the dominant contributors.

In ring-systems with fewer than three rings, ab initio calculations suggest that aromaticity contributes little to stacking forces, and that the strength of these forces, which stabilise the stacked conformation, does not differ significantly from the van der Waals forces also experienced by similarly-sized saturated molecules when stacked. Therefore DNA nucleobases (having one or two rings) probably do not significantly stabilise DNA's stacked structure as a result of their aromaticity, but do so by those intermolecular forces experienced by all closed-shell neutral molecules.

For larger ring-systems (perhaps including twelve or more atoms), there does appear to be such a π-π effect, caused by a larger orbital-dependent (ie non-atom-pairwise) contribution to the dispersion component of the van der Waals force than in an equivalent saturated molecule. This contribution is coupled with the optimal stacking of π-orbitals minimising exchange 'repulsion' for geometric reasons. Electrostatic forces actually considerably weaken this effect in aromatics, though do not entirely cancel it, whereas the induction component of van der Waals forces makes no significant contribution.

The rest of this article has not yet been updated to reflect this research.^[3].

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Crystal structure of a fullerene bound in abuckycatcher through aromatic stacking interactions. Reported by Sygula and coworkers.^[2]

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Stacking within supramolecular chemistry

In supramolecular chemistry, an aromatic interaction (orπ-π interaction) is a noncovalent interaction between organic compounds containing aromatic moieties. π-π interactions are caused by intermolecular overlapping of p-orbitals in π-conjugated systems, so they become stronger as the number of π-electrons increases. Other noncovalent interactions include hydrogen bonds, van der Waals forces, charge-transfer interactions, and dipole-dipole interactions.

π-π interactions act strongly on flat polycyclic aromatic hydrocarbons such as anthracene, triphenylene, andcoronene because of the many delocalized π-electrons. This interaction, which is a bit stronger than other noncovalent interactions, plays an important role in various parts of supramolecular chemistry. For example, π-π interactions have a large influence on molecule-based crystal structures of aromatic compounds.

A powerful demonstration of stacking is found in the buckycatcher depicted below.^[2] This molecular tweezer is based on two concave buckybowls with a perfect fit for one convex fullerene molecule. Complexation takes place simply by evaporating a toluene solution containing both compounds. In solution an association constant of 8600 M^-1 is measured based on changes in NMRchemical shifts.

Stacking in biology

In DNA, pi stacking occurs between adjacent nucleotides and adds to the stability of the molecular structure. The nitrogenous bases of the nucleotides are made from either purine or pyrimidine rings, consisting of aromatic rings. Within the DNA molecule, the aromatic rings are positioned nearly perpendicular to the length of the DNA strands. Thus, the faces of the aromatic rings are arranged parallel to each other, allowing the bases to participate in aromatic interactions. Through aromatic interactions, the pi bonds, extending from atoms participating in double bonds, overlap with pi bonds of adjacent bases. This is a type of non-covalentchemical bond. Though a non-covalent bond is weaker than a covalent bond, the sum of all pi stacking interactions within the double-stranded DNA molecule creates a large net stabilizing energy.

Uses in materials

Many discotic liquid crystals can form columnar structures by π-π interactions. In addition, π-π interactions are an important factor in molecular self-assembly techniques in bottom-up nanotechnology.

Aromatic stacking interaction

Aromatic stacking interaction, sometimes called phenyl stacking, is a phenomenon in organic chemistry that affects aromaticcompounds and functional groups. Because of especially strong Van der Waals bonding between the surfaces of flat aromatic rings, these groups in different molecules tend to arrange themselves like a stack of coins. This bonding behavior affects the properties ofpolymers as diverse as aramids, polystyrene, DNA, RNA, proteins, and peptides. The effect can be exploited in gas sensors to detect the presence of aromatic chemicals.

T-stacking

A related effect called T-stacking is often seen in proteins where the partially positively charged hydrogen atom of one aromatic system points perpendicular to the center of the aromatic plane of the other aromatic system. This is also known as an edge-face interaction.

External links

The physical basis of nucleic acid base stacking in water.

References

^ A. Petitjean, R. G. Khoury, N. Kyritsakas and J. M. Lehn (2004). "Dynamic Devices. Shape Switching and Substrate Binding in Ion-Controlled Nanomechanical Molecular Tweezers". J. Am. Chem. Soc. 126 (21): 6637–6647. doi:10.1021/ja031915r.
^ ^a ^b A. Sygula, F. R. Fronczek, R. Sygula, P. W. Rabideau and M. M. Olmstead (2007). "A Double Concave Hydrocarbon Buckycatcher". J. Am. Chem. Soc. 129 (13): 3842–3843. doi:10.1021/ja070616p.
^ Angew. Chem. Int. Ed. 2008, 47, 3430 - 3434