Archive for May, 2015

Host-guest complexes

Grimme and coworkers have a featured article on computing host-guest complexes in a recent ChemComm.1 They review the techniques his group has pioneered, particularly dispersion corrections for DFT and ways to treat the thermodynamics in moving from electronic energy to free energy. they briefly review some studies done by other groups. They conclude with a new study of eight different host guest complexes, three of which are shown in Figure 1.




Figure 1. TPSS-D3(BJ)/def2-TZVP optimized structures of 1-3.

These eight host-guest complexes are fairly large systems, and the computational method employed means some fairly long computations. Geometries were optimized at TPSS-D3(BJ)/def2-TZVP, then single point energy determined at PW6B95-D3(BJ)/def2-QZVP. Solvent was included using COSMO-RS. The curcurbituril complex 2 includes a counterion (chloride) along with the guest adamantan-1-aminium. Overall agreement of the computed free energy of binding with the experimental values was very good, except for 3 and the related complex having a larger nanohoop around the fullerene. The error is due to problems in treating the solvent effect, which remains an area of real computational need.

An interesting result uncovered is that the binding energy due to dispersion is greater than the non-dispersion energy for all of these complexes, including the examples that are charged or where hydrogen bonding may be playing a role in the bonding. This points to the absolute necessity of including a dispersion correction when treating a host-guest complex with DFT.

As an aside, you’ll note one of the reasons I was interested in this paper: 3 is closely related to the structure that graces the cover of the second edition of my book.


(1) Antony, J.; Sure, R.; Grimme, S. "Using dispersion-corrected density functional theory to understand supramolecular binding thermodynamics," Chem. Commun. 2015, 51, 1764-1774, DOI: 10.1039/C4CC06722C.

Grimme &host-guest Steven Bachrach 12 May 2015 1 Comment

Uthrene, the smallest diradical graphene fragment

Uthrene 1 is the smallest formally diradical fragment of graphene; it cannot be expressed in a closed shell, fully electron-paired Kekule form. Its isomer zethrene 2 on the other hand, can be expressed in closed shell form.

Melle-Franco has examined these, and related, polycyclic aromatic hydrocarbons with DFT.1 The optimized structure of singlet and triplet 1 at CAM-B3LYP/6-31g(d,p) are shown in Figure 1. The singlet-triplet energy gap of 2 is 16.5 kcal mol-1 with a ground state singlet. However, for 1 the triplet is predicted to be lower in energy than the singlet by 7.7 kcal mol-1. And this gap increases to 10.9 kcal mol-1 at CASSCF(14,14)/6-31g(d,p)//CAM-B3LYP/6-31g(d,p). Natural orbital population analysis of the singlet of 1 at CASSCF identifies two orbitals with populations around 1 e.

Interestingly, both the singlet and triplet of 1 are not planar, exhibiting a twist to avoid the clashing of the hydrogens in the bay region. (This twisting is best seen by clicking on the structures in Figure 1, and viewing the molecules interactively through Jmol.)



Figure 1. CAM-B3LYP/6-31g(d,p) optimized geometries of the singlet and triplet of 1.


(1) Melle-Franco, M. "Uthrene, a radically new molecule?," Chem. Commun. 2015, 51, 5387-5390, DOI: 10.1039/C5CC01276G.


1: InChI=1S/C24H14/c1-5-15-7-3-11-20-22(15)17(9-1)13-19-14-18-10-2-6-16-8-4-12-21(23(16)18)24(19)20/h1-14H

2: InChI=1S/C24H14/c1-5-15-7-3-11-19-22-14-18-10-2-6-16-8-4-12-20(24(16)18)21(22)13-17(9-1)23(15)19/h1-14H

Aromaticity Steven Bachrach 04 May 2015 1 Comment