Modeling Soft Supramolecular Nanostructures by Molecular Simulations

Tânia F. Cova, Sandra C. Nunes, Bruce F. Milne, Andreia F. Jorge, Alberto C. Pais

Research output: Chapter in Book/Report/Conference proceedingChapter


The design and assembly of soft supramolecular structures based on small building blocks are governed by non-covalent interactions, selective host-guest interactions, or a combination of different interaction types. There is a surprising number of studies supporting the use of computational models for mimicking supramolecular nanosystems and studying the underlying patterns of molecular recognition and binding, in multi-dimensional approaches. Based on physical properties and mathematical concepts, these models are able to provide rationales for the conformation, solvation and thermodynamic characterization of this type of systems. Molecular dynamics (MD), including free-energy calculations, yield a direct coupling between experimental and computational investigation. This chapter provides an overview of the available MD-based methods, including path-based and alchemical free-energy calculations. The theoretical background is briefly reviewed and practical instructions are introduced on the selection of methods and post-treatment procedures. Relevant examples in which non-covalent interactions dominate are presented.
Original languageEnglish
Title of host publicationMolecular Dynamics
EditorsAlexander Vakhrushev
Place of PublicationRijeka
ISBN (Electronic)978-1-83881-503-5
ISBN (Print)978-1-78923-524-1
Publication statusPublished - 1 Aug 2018

Bibliographical note

The authors acknowledge the Fundação para a Ciência a Tecnologia (FCT), Portuguese Agency for Scientific Research, through the Projects n. 016648 POCI-01-0145-FEDER-016648 and COMPETE POCI-01-0145-FEDER-007440. The Coimbra Chemistry Centre is also supported by FCT through the Projects PEst-OE/QUI/UI0313/2014 and POCI-01-0145-FEDER-007630. Tânia F.G.G. Cova, Sandra C. C. Nunes and Andreia. F. Jorge acknowledge, respectively, the PhD and post-doctoral research Grants SFRH/BD/95459/2013, SFRH/BPD/71683/2010 and SFRH/BPD/104544/2014, assigned by FCT.


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