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AGGREGATES: Finding structures in simulation results of solutions.

Carlos E S Bernardes1

  • 1Centro 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.

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PubMed
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This study introduces AGGREGATES, a program for analyzing molecular clusters from simulations. It helps understand molecular assembly and properties by calculating cluster statistics and conformations.

Keywords:
4′-hydroxyacetophenoneaggregationionic liquidsnucleationpolymorphismsolutionstructure

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Area of Science:

  • Computational chemistry and materials science.
  • Molecular modeling and simulation analysis.

Background:

  • Molecular Dynamic (MD) and Monte-Carlo (MC) simulations are crucial for studying molecular-level properties of matter.
  • Extracting meaningful data from complex simulation outputs, particularly concerning molecular clusters, remains a significant challenge.

Discussion:

  • The AGGREGATES program identifies and analyzes molecular clusters in simulation trajectories using distance criteria.
  • It computes statistical and shape properties of these clusters, offering insights into their organization.
  • A novel First Shell Analysis method is introduced to identify atomic contacts between molecules within clusters.

Key Insights:

  • AGGREGATES provides essential tools for characterizing molecular clusters and their local environments.
  • The First Shell Analysis facilitates the study of molecular assembly, crystal nucleation, and colloidal particle formation.
  • The program aids in investigating polymorphism, particularly in organic compounds.

Outlook:

  • Further development of AGGREGATES could enhance its utility in diverse fields of molecular simulation.
  • Application of AGGREGATES to complex systems will deepen our understanding of self-assembly and material properties.
  • The program serves as a valuable asset for researchers in computational chemistry and condensed matter physics.