Insights into Noncovalent Binding Obtained from Molecular Dynamics Simulations

• Published in: Chemie ingenieur technik Vol. 90; no. 11; pp. 1864 - 1875
• Main Authors: Baz, Jörg, Gebhardt, Julia, Kraus, Hamzeh, Markthaler, Daniel, Hansen, Niels
• Format: Journal Article
• Language: English
• Published: 01.11.2018
• Subjects: Cyclodextrin; Force field; Free energy; Molecular dynamics simulations; Validation
• ISSN: 0009-286X; 1522-2640
• DOI: 10.1002/cite.201800050

The key to nanoscale control of physical, chemical, and biological processes lies in well‐founded models of noncovalent binding. Atomistic simulations probe the free‐energy surface underlying molecular assembly processes in solution. Two examples of noncovalent binding studied by molecular dynamics simulations are discussed, the dimerization of a water‐soluble perylene bisimide derivative in aqueous solution with a focus on the influence of solvent composition on the aggregation strength and the binding of 1‐butanol to α‐cyclodextrin at infinite dilution with the focus on the determination of method‐independent binding free energies. The association of molecular building blocks in a given solvent depends in a complex manner on the solvent composition. Molecular dynamics simulations provide a molecular‐level understanding of the various driving forces. In this work, two examples of noncovalent binding are studied and some aspects of force field validation are illustrated.