Cycloparaphenylenes (CPP) can serve as both guest and host in a complex. Geometric analysis indicates that optimal binding occurs when the CPP nanohoops differ by five phenyl rings. Employing C-PCM(THF)/ωB97X-D/6-31G(d) computations, we find that the strongest binding does occur when the host and guest differ by five phenyl rings. The guest CPP is modestly inclined relative to the plane of the host CPP except when the host and guest differ by four phenyl rings, when the inclination angle becomes >40°. The distortion/interaction model shows that interaction dominates and is best when the host and guest differ by five phenyl rings. The computed 1H NMR shifts of the guest CPP are shifted by about 1 ppm upfield relative to their position when unbound. This distinct chemical shift should aid in experimental detection of these CPP planetary orbit complexes.

DFT (ωB97X-D, B3LYP-D3, M06-2x, and B3LYP) along with MP2 computations were performed on four cyclophanes composed of two or three cyclooctatetraene (COT) rings connected by two, four, or eight ethylene bridges. Both COT rings in cyclophanes with two ethylene bridges (2) and with four bridges in the 1, 2, 5, and 6 positions (6) are in a tub conformation. However, the cyclophane with the four bridges in the 1, 3, 5, and 7 positions (7) is notable for the near planar geometry of the COT rings. The triple-decker cyclophane 8 has planar top and bottom COT rings, while the central ring is puckered with alternating carbon positions up and down. The nature of the COT rings, especially their antiaromatic character, is assessed using NICS and bond alternation and the distance between the centers of the COT rings.

Analogues of ExBox4+ 1 are proposed that possess triaryl fragments that are nearly flat. These two new hosts are predicted by density functional theory (ωB97X-D/6-311G(d,p)) to bind five small linear acenes more tightly than does 1. The “flatter” triaryl fragments provide a less congested interior along with improved π–π-stacking between these hosts and guests.

The conformational space of 1,4-butanediol was examined at ωB97X-D/6-311+G(d,p). Of the 65 conformers examined, the seven lowest energy conformations have an internal hydrogen bond. The strength of this hydrogen bond is estimated to be 4 kcal mol–1. A broad variety of microsolvated configurations of both the open form 5o and hydrogen-bonded form 5r of 1,4-butanediol involving one to four water molecules were located at ωB97X-D/6-311+G(d,p). When one to three water molecules are included in the clusters, the lowest energy configurations involve the hydrogen-bonded form 5r. With four water molecules, configurations involving the open form 5o are favored enthalpically, but configurations with the hydrogen bonded form 5r are the lowest in free energy. These calculations suggest that both 5r and 5o will coexist in aqueous solution.

To assess the role that electrostatic interactions play in the binding of polycyclic aromatic hydrocarbons within ExBox4+ 1, we report ωB97X-D/6-311G(d,p) computations of the binding of five small linear acenes with the hydrocarbon neutral analogue 5 in both the gas phase and acetonitrile solution. The terphenyl units of 5 are less bowed outward than are the ExBIPY units of 5, due to the lack of charge repulsion. This manifests in a much smaller ring strain energy in 5 than 1. The acenes bind to both 1 and 5 with increasing affinity as the size of the guest increases. The affinity of the PAHs to 1 is greater than the affinity to 5, though the difference in the binding enthapies to 1 and 5 is relatively small, ranging from 2.4 to 9.8 kcal mol–1. Electrostatics account for only 10–20% of the total binding energy.

Extended hydrogen-bonding networks as a mechanism for creating superbases is explored through six different amine scaffolds: linear acenes, cyclohexane, decalin, triptycene, adamantane, and [2.2]paracyclophane. The gas-phase proton affinities of 21 different potential superbases were computed at the ωB97X-D/6-311+G(2d,p) level. This method was benchmarked against the experimental proton affinities of 44 nitrogen bases. Extended hydrogen-bonding networks, including second- and third-layer hydrogen bonding, led to bases with proton affinities 20 kcal mol–1 greater than that of bis(dimethylamino)naphthalene. The strongest bases are the decalin base 25 and the adamantane base 31.

The structures of ExBox4+ 1 and its host–guest complexes with the linear acenes benzene, naphthalene, anthracene, and tetracene were optimized using DFT (ωB97X-D/6-311G(d,p)) in both the gas and solution phases. The structure of 1 systematically varies as it moves from the gas to solution to the solid phase: the outward bending of the triaryl fragment diminishes in this series. The structures of the complexes with anthracene and tetracene are in very good agreement with their X-ray structures. The gas phase binding energy is linearly related to the size of the acene, with the binding free energy of all complexes predicted to be exoergonic in both gas and solution phases.

New superbases, those organic compounds whose basicities are greater than that of proton sponge, are suggested that involve extended hydrogen-bonding networks. Addition of aminoethyl and related groups to the 1,8-diaminonaphthalene framework provide second- and third-layer hydrogen bonding in the conjugate base. DFT computations predict these compounds to be 10–15 kcal mol–1 more basic than the proton sponge.

Direct dynamics trajectory simulations were performed for two examples of the thiolate-disulfide exchange reaction, that is, HS– + HSSH and CH3S– + CH3SSCH3. The trajectories were computed for the PBE0/6-31+G(d) potential energy surface using both classical microcanonical sampling at the ion-dipole complex and quasi-classical Boltzmann sampling (T = 300 K) at the central transition state. The potential energy surface for these reactions involves a hypercoordinate sulfur intermediate. Despite the fact that the intermediate resides in a shallow well (less than 5 kcal/mol), very few trajectories follow a direct substitution path (the SN2 pathway). Rather, the mechanism is addition–elimination, with several trajectories sampling the intermediate for long times, up to 15 ps or longer.

The three smallest symmetrical paracyclophanes, having tethers with two, three, or four methylene groups, have been examined with four density functional methods (B3LYP, M06-2x, B97-D, ωB97X-D). The geometries predicted by functionals accounting for medium-range correlation or long-range exchange and/or dispersion are in close agreement with experiment. In addition, these methods provide similar estimates of the strain energy of the paracylcophanes, which decrease with increasing tether length. [4.4]Paracyclophane is nearly strain-free, reflecting the small out-of-plane distortion of its phenyl rings. Lastly, the barrier for interconversion of the conformers of [3.3]paracylcophane is computed in close agreement with experiment, and an estimate for phenyl rotation in [4.4]paracyclophane of about 19 kcal mol−1 is predicted by the DFT methods employed.

The effect of microsolvation on the deprotonation energies of uracil was examined using DFT. The structures of uracil and its N1 and N3 conjugate bases were optimized with zero to six associated water molecules. Multiple configurations (upward of 93) of these hydrated clusters were located at PBE1PBE/6-311+G(d,p). Trends in these geometries are discussed, with the waters generally forming chains with small numbers of waters (one–three), rings (three–five waters), or cages (five–six waters). The difference in energy between the N1 and N3 conjugate bases is 13 kcal mol–1 in the gas phase, and it decreases with each added water up to four. At this point the energy difference has been halved, but addition of a fifth or sixth water has little effect on the energy difference. This is understood in terms of the water structures and their ability to stabilize the negatively charged atoms in the conjugate bases.

Microsolvation of the neutral, zwitterion, and unconventional zwitterion (formed by the proton transfer from the thiol to the amine group) was performed using PBE1PBE/6-311+G(d,p) calculations. A large sampling of the configurations of the clusters involving one to six water molecules was created by analogy to glycine clusters and through analysis of hydrogen-bonding trends. Clusters of the neutral tautomer are lowest in energy with the inclusion up to five water molecules. With six water molecules the neutral and zwitterion are nearly isoenergetic. The unconventional zwitterion, while a stable structure when at least one water molecule is associated with it, remains energetically noncompetitive with the other two tautomers regardless of the degree of microsolvation.

Biphenylene is subject to a variety of destabilizing effects (antiaromaticity, ring strain) and resonance stabilization. Careful construction of a group equivalent reaction that isolates the destabilization energy from other chemical effects, notably resonance energy, leads to a revised estimate of the destabilization energy of biphenylene as 57 kcal mol−1. Extension of these ideas to higher homologoues of biphenylene, including starphenylene, point out pitfalls of any approach toward uniquely defining reactions that measure chemical effects.

MP2/aug-cc-pVDZ and B3LYP/cc-pVDZ calculations of the reactions of CH3SSR (R = H or CH3) with fluoride, hydroxide or allyl anion in the gas-phase were performed to determine the mechanism for both elimination and substitution reactions. The elimination reactions were shown to follow the E2 mechanism. The substitution reactions with hydroxide and fluoride proceed by the addition–elimination mechanism, but those with allyl anion proceed by the SN2 mechanism. The elimination reactions with F− and HO− are preferred to the substitution reactions, while allyl anion prefers the substitution route.