Reversibly controllable guest binding in precisely defined cavities: selectivity, induced fit, and switching in novel resorcin[4]arene-based container molecules

Two molecular baskets are presented, which were constructed based on a resorcin[4]arene platform. The molecules completely surround suitable guests, such as cyclo- or oxacycloalkanes, and bind them with high strength. The thermodynamic parameters for inclusion complexation were determined as well as the influence of encapsulation on the ring inversion barrier of bound cyclohexane. Two-dimensional NMR spectroscopy clearly shows the existence of a directed attractive interaction between oxacyclohexane and one of the hosts, which constrains the rotation of the bound molecule. Both containers exhibit remarkable binding selectivity as a consequence of their precisely defined structures. They both differentiate between homologous cycloalkanes, and whereas cyclohexane binds best within the larger of the two interior cavities, cyclopentane fits best in the smaller one. The selectivity is governed by ideal filling of space. We have conducted molecular dynamics experiments to understand the thermal fluctuations in the cavity sizes when a guest is bound. The simulations show that within a very narrow range the hosts adapt their binding site to different guests in order to optimize the fraction of occupied space. Once a binding geometry is established, it is characterized by a very low degree of flexibility. The guest-hosting properties of both molecules can be suspended by an external stimulus: addition of acid induces an opening of portals in the structures and immediately releases all bound cat-go. Neutralization of the solution completely restores the initial state. (C) 2008 Elsevier Ltd. All rights reserved

Structures and stabilities of diacetylene-expanded polyhedranes by quantum mechanics and molecular mechanics

The structures, heats of formation, and strain energies of diacetylene (buta-1,3-diynediyl) expanded molecules have been computed with ab initio and molecular mechanics calculations. Expanded cubane, prismane, tetrahedrane, and expanded monocyclics and bicyclics were optimized at the HF/6-31G(d) and B3LYP/6-31G(d) levels. The heats of formation of these systems were obtained from isodesmic equations at the HF/6-31G(d) level. Heats of formation were also calculated from Benson group equivalents. The strain energies of these expanded molecules were estimated by several independent methods. An adapted MM3* molecular mechanics force field, specifically parametrized to treat conjugated acetylene units, was employed for one measure of strain energy and as an additional method for structural analysis. Expanded dodecahedrane and icosahedrane were calculated by this method. Expanded molecules were considered structurally in the context of their potential material applications

Butatrienes as extended alkenes: Barriers to internal rotation and substitution effects on the stabilities of the ground states and transition states

The barriers to internal rotation of methylated, ethynylated, and vinylated butatrienes and alkenes were calculated at the CASPT2/6-31G(d)//B3LYP/6-31G(d) level. Calculated butatriene rotational barriers are lower than those of analogous alkenes, but there is a larger variance in rotational barrier for alkenes than for butatrienes. The barriers to rotation were analyzed by isodesmic equations designed to estimate the substituent effects in the ground (GS) and transition (TS) states individually. The GSs of both series are stabilized to roughly the same extent. In contrast, the TSs of butatrienes are more stabilized overall than those of alkenes. Much of the stabilization in the TS of butatrienes comes from the internal triple bond and not from the substituent. Estimation of the substituent stabilization alone reveals the TSs of ethylenes to be more stabilized by substitution than butatrienes

Butatrienes as extended alkenes: Barriers to internal rotation and substitution effects on the stabilities of the ground states and transition states

The barriers to internal rotation of methylated, ethynylated, and vinylated butatrienes and alkenes were calculated at the CASPT2/6-31G(d)//B3LYP/6-31G(d) level. Calculated butatriene rotational barriers are lower than those of analogous alkenes, but there is a larger variance in rotational barrier for alkenes than for butatrienes. The barriers to rotation were analyzed by isodesmic equations designed to estimate the substituent effects in the ground (GS) and transition (TS) states individually. The GSs of both series are stabilized to roughly the same extent. In contrast, the TSs of butatrienes are more stabilized overall than those of alkenes. Much of the stabilization in the TS of butatrienes comes from the internal triple bond and not from the substituent. Estimation of the substituent stabilization alone reveals the TSs of ethylenes to be more stabilized by substitution than butatrienes

Importance of correlated motions on the low barrier rotational potentials of crystalline molecular gyroscopes

The energetic and structural changes taking place upon rotation of the central phenylene of 1,4-bis(3,3,3-triphenylpropynyl)benzene in the solid state were computed using molecular mechanics calculations. Pseudopolymorphic crystals of a benzene clathrate (1A) and a desolvated form (1B) were analyzed with models that account for varying degrees of freedom within the corresponding lattices. The calculated rotational barriers in a rigid lattice approximation, 78 kcal/mol for 1A and 72 kcal/mol for 1B, are about 5 times greater than those previously measured by variable-temperature C-13 CPMAS NMR and quadrupolar echo H-2 NMR line-shape analysis: 12.8 kcal/mol for 1A and 14.6 kcal/mol for 1B. The potential energy barriers calculated with a model that restricts whole body rotation and translational motions but allows for internal rotations give results that are near the experimental free-energy barriers. The calculated barriers for 1A and 1B are 15.5 and 16.2 kcal/mol, respectively. The differences between the rigid and partially relaxed models are attributed to the effect of correlated motions of the lattice and the rotating group, which are evident from the structural analysis of the atomic position data as a function of the dihedral angle of the rotator. The displacements of neighboring molecules near the rotary transition states for 1A and 1B can be as large as 2.7 and 1.1 A, respectively. The displacement and oscillation (C-2) of interpenetrating phenyl rings from neighboring rotors proximal to the event are significant for both 1A and 1B. In addition, 6-fold (C-6) benzene rotations in clathrate 1A were found to be directly correlated to the rotation of the phenylene rotator