Encapsulation of Methane and Other Small Molecules in a Self-Assembling Superstructure

Branda, Neil R.; Wyler, R.; Rebek, Jr. Julius

doi:10.1126/science.8122107

Cited by 196 publications

(128 citation statements)

References 15 publications

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“…80 The inner volume of the capsule (∼50 Å 3 ) is rather small and only allows for the encapsulation of small molecules such as methane and noble gases. To complex larger guests, the spacers between the glycoluril moieties were varied, generating a number of dimeric and higher order capsules with inner compartments of varying sizes.…”

Section: Noncovalent Systemsmentioning

confidence: 99%

Self-Assembled Nanoreactors

et al. 2005

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Section: Noncovalent Systemsmentioning

confidence: 99%

Self-Assembled Nanoreactors

et al. 2005

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“…The system we have selected to study is a model for a protein ligand-binding cavity based on a selfassembling superstructure, the "tennis ball"dimer ( Figure 1). We have chosen this model as it combines simplicity with realism and also because there are previous computational 15 studies and experimental 16 data to compare with. We first compare structure optimization with a force field and first principles approaches in terms of the structural parameters.…”

Section: Articlementioning

confidence: 99%

First Principles-Based Calculations of Free Energy of Binding: Application to Ligand Binding in a Self-Assembling Superstructure

Fox

Wallnoefer

Fox

et al. 2011

J. Chem. Theory Comput.

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The accurate prediction of ligand binding affinities to a protein remains a desirable goal of computational biochemistry. Many available methods use molecular mechanics (MM) to describe the system, however, MM force fields cannot fully describe the complex interactions involved in binding, specifically electron transfer and polarization. First principles approaches can fully account for these interactions, and with the development of linear-scaling first principles programs, it is now viable to apply first principles calculations to systems containing tens of thousands of atoms. In this paper, a quantum mechanical PoissonBoltzmann surface area approach is applied to a model of a protein-ligand binding cavity, the "tennis ball" dimer. Results obtained from this approach demonstrate considerable improvement over conventional molecular mechanics Poisson-Boltzmann surface area due to the more accurate description of the interactions in the system. For the first principles calculations in this study, the linear-scaling density functional theory program ONETEP is used, allowing the approach to be applied to receptor-ligand complexes of pharmaceutical interest that typically include thousands of atoms.

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“…The building blocks that are widely used for the preparation of molecular cages include (among others): calixarenes [9,10], resorcinarenes [11,12], glycorils [13,14], and spherands [15]. In order to facilitate the formation of the cage and avoid side compounds, preorganisation of the subunits is necessary and the use of template compounds is usually recommended [13,14,16,17].…”

Section: Introductionmentioning

confidence: 99%

Theoretical study of the geometrical and electronic structures and thermochemistry of spherophanes

et al. 2009

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A set of supramolecular cage-structuresspherophanes-was studied at the density functional B3LYP level. Full geometrical structure optimisations were made with 6-31G and 6-31G(d) basis sets followed by frequency calculations, and electronic energies were evaluated at B3LYP/6-31++G(d,p). Three different symmetries were considered: C1, Ci, and Oh. It was found that the bonds between the benzene rings are very long to allow π-electron delocalisation between them. These spherophanes show portal openings of 2.596 Å in Spher1, 4.000 Å in Meth2, 3.659 Å in Oxa3, and 4.412 Å in Thia4. From the point of view of potential host-guest interaction studies, it should also be noted that the atoms nearest to the centre of the cavities are carbons bonded to X groups. These supramolecules seem to exhibit relatively large gap HOMO−LUMO: 2.89 eV(Spher1),

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Encapsulation of Methane and Other Small Molecules in a Self-Assembling Superstructure

Cited by 196 publications

References 15 publications

Self-Assembled Nanoreactors

Self-Assembled Nanoreactors

First Principles-Based Calculations of Free Energy of Binding: Application to Ligand Binding in a Self-Assembling Superstructure

Theoretical study of the geometrical and electronic structures and thermochemistry of spherophanes

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