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Self-Inclusion Complexes of Monofunctionalized Beta-Cyclodextrins as Host–Guest Interaction Model Systems and Simple and Sensitive Testbeds for Implicit Solvation Methods

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Computational Electrostatics for Biological Applications

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Abstract

The validation of biomolecular computational approaches represents a critical step to assess their general reliability and possible fields of application. However, it requires a combined selection of protocols and representative model systems which needs great attention, since both choices can bias the results, or alter the method sensitivity to the numerous parameters that describe the systems. Here we propose the use of self-included monofunctionalized \(\beta \)-cyclodextrins (mf-\(\beta \)-CDs) to evaluate and compare solvation methods. For that end, we characterized the self-inclusion processes of three mf-\(\beta \)-CDs by molecular dynamics simulations performed with both explicit solvent and three implicit solvent implementations based on the generalized Born approach. In particular, we monitored the sensitivity to the different solvation models of the resulting trajectories and of several structural and energetic parameters usually adopted to study cyclodextrins or solvation methods. Our results confirmed that mf-\(\beta \)-CD are useful testbeds to compare solvation approaches because their properties are particularly affected by the relative stabilities of hydrophobic versus polar interactions and by energy contributions implicitly or explicitly dependent on exposed molecular surfaces.

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Authors and Affiliations

  1. Institute of Biomolecular Chemistry of the National Research Council of Italy (ICB-CNR), Via Campi Flegrei 34, 80078, Pozzuoli, NA, Italy

    Rosa Maria Vitale & Pietro Amodeo

Authors
  1. Rosa Maria Vitale
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  2. Pietro Amodeo
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Correspondence to Pietro Amodeo .

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Editors and Affiliations

  1. CONCEPT Lab - CompuNet, Istituto Italiano di Tecnologia, Genova, Italy

    Walter Rocchia

  2. Institute of Applied Mathematics and Inf, National Research Council, Genova, Italy

    Michela Spagnuolo

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Vitale, R.M., Amodeo, P. (2015). Self-Inclusion Complexes of Monofunctionalized Beta-Cyclodextrins as Host–Guest Interaction Model Systems and Simple and Sensitive Testbeds for Implicit Solvation Methods. In: Rocchia, W., Spagnuolo, M. (eds) Computational Electrostatics for Biological Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-12211-3_14

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