title: AGGREGATES: Finding structures in simulation results of solutions.
abstract: Molecular Dynamic and Monte-Carlo simulations are widely used to investigate the structure and physical properties of solids and liquids at a molecular level. Tools to extract the most relevant information from the obtained results are, however, in considerable demand. One such tool, the program AGGREGATES, is described in this work. Based on distance criteria, the program searches trajectory files for the presence of molecular clusters and computes several statistical and shape properties for these structures. Tools designed to investigate the local organization and the molecular conformations in the clusters are also available. Among these, it is introduced a new approach to perform a First Shell Analysis, by looking for the presence of atomic contacts between molecules. These elements are particularly useful to obtain information on molecular assembly processes (such as the nucleation of crystals or colloidal particles) or to investigate polymorphism in organic compounds. The program features are illustrated here through the investigation of the 4'-hydroxyacetophenone + ethanol system. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Portugal 1749-016 Lisboa; Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, 1049-001, Portugal.
authors.forename: Carlos E S
authors.identifier: 0000-0003-1490-9728
authors.initials: CE
authors.lastname: Bernardes
keywords: 4′-hydroxyacetophenone; aggregation; ionic liquids; nucleation; polymorphism; solution; structure