Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 38, Issue 10, Pages 753-765Publisher
WILEY
DOI: 10.1002/jcc.24735
Keywords
aggregation; nucleation; polymorphism; ionic liquids; 4 '-hydroxyacetophenone; solution; structure
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Funding
- Fundacao para a Ciencia e a Tecnologia (FCT), Portugal [UID/MULTI/00612/2013, UID/QUI/00100/2013]
- FCT (A Post-doctoral grant) [SFRH/BPD/101505/2014]
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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 40-hydroxyacetophenone + ethanol system. (C) 2017 Wiley Periodicals, Inc.
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